The Franciscan monastery (Sacro Convento) and the lower and upper church (Basilica inferiore e superiore) of St Francis were begun immediately after his canonization in 1228. Simone di Pucciarello donated the land for the church, a hill at the west side of Assisi, known as "Hill of Hell" (because here the criminals were put to death). Today, this hill is aptly called "Hill of Paradise".
The foundation stone was laid by Pope Gregory IX on 17 July 1228, although construction may already have been begun. This impressive church was designed and supervised by brother Elia Bombardone, one of the first followers of St. Francis and the former provincial minister of Syria. The lower basilica was finished in 1230. On Pentecost 25 May 1230 the uncorrupted body of St. Francis was brought in a solemn procession to the lower basilica from its temporary burial place in the church of St. George (now the basilica of St. Clare). The construction of the upper basilica was began after 1239. Construction was completed in 1253. Its architecture is a synthesis of Romanesque and French Gothic artwork, establishing many of the typical characteristics of Italian Gothic architecture.
The churches have been decorated by the greatest late medieval Roman, Umbrian and Tuscan artists of their time, giving these churches an unequalled importance in the development of Italian art. The lower church has frescos by renowned late-medieval artists, such as Cimabue and Giotto; in the upper church are a series frescoes depicting scenes in the life of St Francis attributed to Giotto and his circle.
Pope Nicholas IV, the former Master-General of the Order of Franciscans, raised the church to the status of papal church in 1288.
The Piazza del Loge, the square leading to the church, is surrounded by colonnades constructed in 1474. They housed the numerous pilgrims flocking to this church.
On 27 October 1986 and January 2002, Catholic pontiff Pope John Paul II gathered in Assisi with the leaders of the great world confessions to pray for peace.
On September 26, 1997 Assisi was struck by an earthquake which caused four fatalities. The Basilica was badly damaged (part of the vault collapsed, carrying with it a fresco by Cimabue), and was closed for two years for restoration.
Brother Elia had designed the lower basilica as an enormous crypt with ribbed vaults. He had acquired his experience by building huge sepulchres out of hard rock in Syria.
Entering the lower basilica via the side portal in Gothic style (second half of the 13th c.) with two wooden doors (Umbrian craftmanship from the 16th c.), one sees at the other side of the vestibule the chapel of Cardinal Egidio Albornoz, papal legate in charge of the Papal States (from 1350 to 1367). It is dedicated to St. Catherine of Alexandria. The frescoes with the eight episodes from the life of St. Catherine were painted in 1368-1369 by ‘Andreas pictor de Bononia’. This painter, called Andrea, is most probably Andrea de’ Bartoli (c. 1349 - 1369), the court artist of Albornoz (and not Andrea da Bologna, as usually, but wrongly, attributed). The saints in this chapel were painted by Pace di Bartolo d'Assisi (1344-1368).
On the left side is the small Chapel of St. Sebastian with a canvas by Giorgetti and episodes of the life of the saint on the walls by G. Martelli. On the right side there are two monuments : the mausuleum of Giovanni de' Cerchi and the mausuleum of John of Brienne, king of Jerusalem and emperor-regent of Constantinople.
The lower basilica consists of a central nave with several side chapels with semi-circular arches. The nave is decorated with the oldest frescoes in the church by an unknown artist, called Maestro di San Francesco. They feature five scenes from the Passion of Christ on the right side, while on the left side equally five scenes from the Life of St. Francis. By this juxtaposition, the Franciscans wanted to contribute to the idea of their founder as a second Christ.
They are connected by a low blue-painted ceiling decorated with golden stars. Most images on the lower walls have decayed to leave almost no trace, except on the right wall fragments of Virgin and Child with an Angel by Cimabue.
These frescoes, executed in tempera on dry plaster, were completed about 1260-1263. They are considered by many as the best examples of Tuscan wall paintings prior to Cimabue. As the popularity of this church increased, side chapels for noble families were added between 1270 and 1350, destroying the frescoes on the opened walls.
The first chapel on the left is dedicated to Saint Martin of Tours. It was built by Cardinal da Montefiore, and was decorated between 1317 and 1319 with ten frescoes depicting his life by Simone Martini and with a polyptych with figures of saints. These are amongst the greatest works of Simone Martini and the finest examples of 14th century painting. The use of lead white has over the years darkened several passages in these works.
The other chapel on the left is dedicated to St. Peter of Alcantara.
The chapels on the right are dedicated to :
-Saint Louis of Toulouse and Saint Stephan with frescoes by Dono Doni (1575) and stained glass, attributed to Simone Martini.
-Saint Anthony of Padua with frescoes by Cesare Sermei (1610,)
-St. Mary Magdalene. This chapel, built by Teobaldo Pontano (bishop of Assisi from 1296 to 1329), contains some of the best works of the workshop of Giotto and maybe by the master himself (about 1320) (wrongly attributed by Vasari to Puccio Capanna). On the lateral walls are scenes from the Life of Mary Magdalene (above the portrait of Teobaldo Pontano), while in the vault there are roundels with busts of Christ, the Virgin, Mary Magdalene and Lazarus.
The nave ends in a richly decorated semicircular apse, preceded with a transept with barrel vaulting.
The frescoes in the right transept depict the childhood of Christ, partly by Giotto and his workshop and the Nativity by the anonymous Maestro di San Nicola. The lowest level shows three frescoes representing St. Francis posthumously intervening in favour of two children. These frescoes by Giotto were revolutionary in their time, showing real people with emotions, set in a realistic landscape.
On the transept wall Cimabue painted his most famous work "Our Lady enthroned and Saint Francis" (1280). This is probably the nearest likeness to St. Francis. This static painting in Gothic style is in stark contrast with the lively frescoes of Giotto.
This right transept also contains the Chapel of Saint Nicolas of Bari, probably commissioned by the papal legate Cardinal Napoleone Orsini. It is decorated with a cycle of 10 frescoes by the (anonymous) Master of the Chapel of St Nicholas (between 1295 and 1305), depicting the miracles and the charity of Saint Nicholas. This cycle has been influenced by the cycle of the Legend of St. Francis in the upper basilica. This confused Vasari into (wrongly) ascribing this frescoes to 'Giottino'. The same master then executed the Annunciation across the entrance of the chapel.
The left transept was decorated by the Sienese painter Pietro Lorenzetti and his workshop between 1315 and 1330 (attributed by Vasari Pietro Lorenzetti and also (wrongly) to Giotto and Puccio Capanna) . This cycle of tempera frescoes are his masterworks. They depict six scenes from the Passion of Christ. Especially the fresco of Deposition of the Cross is highly emotional. In this cycle one can see cast shadows, for the first time since antiquity. There were about 330 work-stages needed to complete this cycle. This means that these frescoes were executed over several years, even with the assistance of his workshop. He also decorated the adjoining chapel of St John the Baptist with the fresco "Madonna dei Tramonti “.
The juxtaposition of the Childhood and the Passion frescoes intend to stress the parallel between the passion of Christ and the compassion of St. Francis.
The papal altar in the apse was made out of one block of stone from Como in 1230. Around the altar are a series of ornamented gothic arches, supported by columns in different styles. The 12 colums that surrounded the altar were removed in 1870. The fine gothic walnut choir stalls were completed in 1471 by Apollonio Petrocchi da Ripatransone, with the help of Tommaso di Antonio Fiorentino and Andrea da Montefalco.
Once featuring frescoes depicting an allegory of the Crucifixion by Stefano Fiorentino (destroyed in 1622), the walls of the apse are now covered with a "Last Judgment" by Cesare Sermei di Orvieto (1609-1668).
The paintings in the lunettes of the vaults (1315-20) depict the "Triumph of St Francis“ and three allegories of Obedience, Poverty and Chastity by the so-called Maestro delle Vele (Master of the Assisi vaults), a pupil of Giotto (about 1330).
The stained glass windows in this lower basilica are attributed to Giovanni di Bonino and his workshop.
Halfway down the nave one can descend into the crypt via a double stairway. This burial place of St. Francis was found again in 1818. His remains had been hidden by brother Elia to prevent the spread of his relics in medieval Europe. By order of Pope Pius IX a crypt was built under the lower basilica. It was designed by Pasquale Belli with precious marble in neo-classical style. But it was redesigned in bare stone in neo-Romanesque style by Ugo Tarchi between 1925 and 1932.
The ancient stone coffin with iron ties is enshrined in an open space above the altar. In 1934 his most faithful brothers were entombed in the corners of the wall around the altar: brother Rufino, brother Angelo, brother Masseo and brother Leone.
At the entrance of the crypt, an urn with the remains of Jacopa dei Settesoli was added to the crypt. This woman of Roman nobility was the most faithful friend and benefactress of St. Francis. She was at his side in the Porziuncola at the hour of his death.
Next to the basilica stands the friary Sacro Convento with its imposing walls with 53 Romanesque arches and powerful buttresses supporting the whole complex. It towers over the valley below, giving the impression of a fortress. It was built with pink and white stone from Mount Subasio. It was already inhabited by the friars in 1230. But construction took a long time, with as result different styles intermingling : Romanesque with Gothic style. A major part was built under the reign of pope Sixtus IV, a franciscan, between 1474 and 1476.
The friary now houses a vast library (with medieval codices and incunables), a museum with works of art donated by pilgrims through the centuries and also the 57 works of art (mainly of Florentine and Sienese schools) of the Perkins collection.
The belfry, in Romanesque style, was finished in 1239.
One enters the upper basilica from the loggia of the friary. The slender Gothic style of the upper basilica gives a completely different impression.
Large glass stained windows, placed halfway up the walls, shed their coloured light on the masterworks of Giotto and Cimabue. The windows in the choir were produced by German craftsmen, active around Assisi in the last part of the 13th century. The windows on the left hand side of the nave were made by a French workshop (1270), while those on the right handside are attributed to the workshop of Maestro di San Francesco. These stained glass windows are among the best examples of 13th c. Italian glasswork.
This bright and spacious basilica consists of a single four-bay nave with cross-vaulted ceiling bordered with patterns of crosses and leaves, a transept and a polygonal apse. The four-ribbed vaults are decorated alternatively with golden stars on a blue background and paintings. The second vault is decorated with roundels with busts of Christ facing St. Francis and the Virgin facing St. John the Baptist. The entrance vault gives us the Four Latin Doctors of the Church : St Gregory facing St Jerome and St Ambrose facing St Augustine. These are ascribed to the Isaac Master.
The choir has 102 wooden stalls with carvings and marquetry by Domenico Indovini (1501). In their centre, on a raised platform, stands the papal cathedra.
The west end of the transept and the apse have been decorated with many frescoes by Cimabue and his workshop (starting in c. 1280). The magnificent Crucifixion, with St. Francis on his knees at the foot of the Cross, stresses again the veneration of the Passion of Christ by St. Francis. Sadly, the frescoes of Cimabue soon suffered from damp and decay. Due to the use of lead oxide in his colours and to the fact that the colours were applied when the plaster was no longer fresh, they have deteriorated and have been reduced to photographic negatives.
Prior to him there had been some decorations in the upper right hand section of the transept by an (anonymous) Northern Master, probably an English artist (1267-1270). He realized the two lunettes and the roundels on the west wall with paintings of the Angel and the Apostles. Another (anonymous) master, the Roman Master, painted the Isaiah and the David and the remainder of the wall under the eastern lunette.
The upper part on both sides of the nave, badly damaged by the earthquake of 1997, was decorated in two rows with in total 32 scenes from the Old Testament (starting with Creation of the World and ending with Joseph forgives his brothers) and the New Testament (from the Annunciation to The Women at the Tomb), while the upper register of the entrance wall is covered with two frescoes Pentecost and Ascension of Jesus. Since it took about six months to paint one bay of the nave, different Roman and Tuscan masters, followers of Cimabue, have performed this series of scenes such as Giacomo, Jacopo Torriti and Pietro Cavallini.
The two frescoes of the life of Isaac (Isaac blesses Jabob and Esau in front of Isaac) in the middle register of the third bay, are traditionally ascribed to the young Giotto (1290-1295) (previously wrongly ascribed to Cimabue by Vasari). But even this has been controversial. Many critics esteem these the work of the anonymous Isaac Master and his workshop. Deducing from stylistic details, attesting to his Roman background, some think that the Isaac Master may have been Pietro Cavallini or a follower. Pietro Cavallini had painted around 1290 a similar fresco Isaac blessing Jacob in the convent of the church Santa Cecilia in Trastevere in Rome. The position of the resting Isaac looks like the same position of the Virgin in Cavallini's mosaic Birth of the Virgin in the apse of the church Santa Maria in Trastevere in Rome. The Isaac Master is considered one of the first practioners of the true fresco (buon fresco) technique.
But the most important decorations are the series of 28 frescoes ascribed to the young Giotto along the lower part of the nave. Each bay contains three frescoes above the dado on each side of the nave, two frescoes in the east galleries beside the entrance, and two more on the entrance wall. Giotto used the Legenda Maior, the biography of St. Francis by St. Bonaventure (1266) to reconstruct the major events in the life of St. Francis. The protoype for this cycle may have been the (now lost) St Francis cyle by Pietro Cavallini in the church San Francesco a Ripa in Rome. The paintings are so vivid, as if Giotto had been a witness to these events. According to Vasari, they were executed in the period between 1296 and 1304.
However the authorship of Giotto is disputed, due to the ambiguous attributions given in early descriptions of this work. Many Italian critics continue to support the authorship of Giotto and his workshop. But because of small differences in style with the frescoes of Isaac, it is thought that several or even all of these frescoes were painted by at least three separate painters, using the original concept of Giotto : the Master of Legend of St. Francis (the principal painter and probable supervisor of the cycle), the Master of the Obsequies of St. Francis and the Cecilia Master.
The first span of the ceiling is decorated with frescoes of the "Four Doctors of the Church" ( Jerome, Augustine, Gregory and Ambrose), attributed either to a young Giotto or to one of his followers. The third span presents four heart-shaped medallions of the Christ, Mary, John the Baptist and Francis, painted by Jacopo Torriti.
The cuspidate façade of the upper basilica has a portal in Gothic style with twin doors and a beautiful rose window.

In the summer of 1205, St. Francis, who had retired for a prayer in the small country oratory, heard the Crucifix (now at St. Clare's) talk to him ordering him to restore the church in decay.
In 1212 St. Clare and her companions established themselves in this place where between 1224-25 St. Francis wrote his Cantico delle Creature (Song of the Creatures).
The Clarisse lived here until they moved to the actual convent in 1260.
The church is preceded by a portico; on its right opens the Chapel of St. Hieronymus (Cappella di S. Girolamo) with frescoes by Tiberio d'Assisi (1517 and 1522).
The single-naved interior has a slightly ogival vault and an apse with fresco decorations of the early 14th century. The Crucifix at the main altar is a copy of the one now at St. Clare's.
The wooden stalls date back to 1504. On the right, a passage leads through a room with a „Crucifiction" by Pier Antonio Mezzastris (1482) to the garden of St. Clare and to the conventual rooms.
In the cloister, frescoes by Eusebio da S. Giorgio (1507), "Stigmatisation of St. Francis" and "Annunciation"; in the refectory, badly preserved frescoes by Dono Doni representing the episode of the Talking Crucifix and St. Clare leaving the signs of the cross on the bread she is blessing.

The earlies records of this building date back to 1174, when it was erected as a German feudal castle.
The future Emperor Frederick II of Swabia spent several years of his childhood here in the care of Conrad of Urslingen, and was baptised in Assisi at the age of three in 1197.
The following year, in Conrad's absence, the people of Assisi rebelled and destroyed the castle.
The castle remained a ruin until 1367, when Cardinal Albornoz rebuilt the fortress using the western section of outside walls and part of the interior fortifications.
In 1458 Jacopo Piccinino, then lord of Assisi, erected the twelve-sided tower and the long curtain wall connecting the castle to the city.
In 1478 Pope Sixtus IV restored the castle's keep, while between 1535 and 1538 Pope Paul III built the round tower near the main gate.

The Basilica of Santa Maria degli Angeli (Saint Mary of the Angels) is a church situated in the plain at the foot of the hill of Assisi.
The basilica was constructed between 1569 and 1679 enclosing the 9th century little church, the Porziuncola, the most sacred place for the Franciscans. It was here that the young Francis of Assisi understood his vocation and renounced the world in order to become a poor among the poor and thus started the Franciscan movement.
After the death of Saint Francis in 1226 , the friars built several small huts around the Porziuncola. In 1230 a refectory and some adjacent buildings were added. In the course of time little porticos and accommodations for the friars were added around the Porziuncola. (some foundations of these were discovered during excavations under the floor of the present basilica between 1967 and 1969).
As more and more vast numbers pilgrims came flocking to Assisi to receive the “Pardon of Assisi”, the small space of the Porziuncola became totally inadequate to house all these pelgrims. The necessity grew to build a church incorporating the Porziuncola. The buildings around the shrine were taken down by order of pope Pius V (1566-72), except the Chapel of the Transito, the cell in which St. Francis had died. Construction of the basilica started on 25 March 1569, This huge, majestuous church, the seventh largest Christian church, was designed, in an Italian pre-Baroque style by the famous architect Galeazzo Alessi (1512-1572), assisted by Jacob Barozzi, also called Vignola (1507-73). The work progressed only due to continuous lack of money, since the building had to be financed with donations. The dome was finished in 1667. This dome, resting on an octogonal drum with eight windows and cornices, is an architectural work of art. Construction of the church was finally finished in 1679. In 1684 a bell tower was added. It was originally intended to have a twin tower, but this was never built.
On 15 March 1832 the central nave, a part of a lateral aisle and the choir collapsed during a violent earthquake. The dome, the only surviving work of Alessi, escaped destruction, but nevertheless had a wide crack. The apse and the side chapels were left standing. Reconstruction of the basilica started in 1836 by the architect Luigi Poletti and it was finished in 1840. He had remodelled the façade in a neoclassical style. Between 1924 and 1930 this façade was given back its original pre-Baroque style by Cesare Bazzani. The gold-plated statue of the "Madonna degli Angeli" (Madonna of the Angels) by the sculptor Colasanti, was put on top of the façade in 1930.
On 11 April, 1909, the church was raised by pope Pius X to the status of "patriarchal basilica and papal chapel"
The basilica has a rectangular ground plan, divided into a central nave and two lateral aisles, flanked by ten side chapels, with at the far end a transept, and a long choir in a semi-circular apse, protruding from the ground plan. The Porziuncola is situated directly under the dome. The church is 126 meters long, 65 meters large and the dome is 75 meters high. The interior is simple and yet elegant with only a few decorations, in stark contrast with the decorations of the side chapels. The nave and the aisles were rebuilt in neoclassical Doric style by Luigi Poletti. The apse holds the precious wooden choir, carved by Franciscan brothers starting in 1689, the papal cathedra (with bas-reliefs by E. Manfrini) and the papal altar. The Chapel of the Transito, the cell in which St. Francis died, is still preserved. It is situated under the bay of the choir, against the right columns of the dome.
The side chapels were decorated by great artists from several periods.
The chiesetta (little church) is the most sacred place for Franciscans. It is considered a holy place. Francis was given this little church, dating from the 9th century, from Benedictine monks.
The church is exquisitely decorated by artists from different periods. Above the entrance is the fresco by Johann Friedrich Overbeck (1829) depicting St Francis receiving from the Christ and the Virgin the indulgence, known as the “Pardon of Assisi”. The side wall on the right side shows fragments of two frescoes by an unknown Umbrian artists.. The austere interior is decorated in a simple Gothic style with frescoes from the 14th and the 15th century. But the masterpiece is the six-part fresco in the apse of this little church, painted by Ilario da Viterbo (1393). At the back, above the entrance, is the fresco “Crucifixion” by Pietro Vannucci, called “the Perugino”.
The Capella del Transito is the small room where St. Francis died on 3 October 1226. It was a little hut serving as a primitive infirmary for the sick. It is decorated at the outside by the fresco “The transito” by Domenico Bruschi (1886). On the inside, above the small altar, is the rope of St. Francis. Behind the altar, there is a glazed terracotta statue of St. Francis by Andrea della Robbia (c. 1490). On the walls there is a fresco by Giovanni Spagna (1520), depicting the earliest followers of St. Francis, with their names above each portrait (Ruffino, Leone, Masseo and Egidio)
A new crypt was constructed behind the altar between 1965 and 1970. During the excavations foundations of the original little huts, surrounding the Porziuncola, were exposed. The crypt’s altar rests on a massive, multiple-branched tree trunk, sculpted by Francesco Prosperi. Behind the altar stands an enameled, terracotta, bas-relief tabernacle by Andrea della Robbia, expressing with an extreme finesse the emotions of the figures : (on top) St Francis receiving the Stigmata, the Coronation of Mary (with the angel musicians), St Jerome the Penitent; (lower section) The Annunciation, the Nativity and the Adoration by the Magi.
One enters the rose garden via the sacristy. It is the last remains of the ancient wood in which St Francis and his friars lived. Here he talked to the turtle doves, inviting them to praise the Lord. Doves have been nesting since times immemorial in the hands of the statue of St. Francis in this rose garden.
According to tradition (already attested at the end of the 13th c.), one night St. Francis, feeling the temptation to abandon his way of life, rolled naked in the bramble thorns in an attempt to attempt over doubt and temptation. In contact with his body, the bramble bushes turned into dog roses without thorns. Since then, the dog rose cultivar Rosa canina 'Assisiensis' has been grown in the garden.
From the rose garden, one enters the Rose Chapel. This was the cell were St. Francis rested and spent the rest of the night in prayer and penance. Here St. Francis also met Saint Anthony of Padua. After his death a chapel was built in the 13th century, enlarged in the 15th c. by St. Bernardine of Siena. It was decorated between 1506 and 1516 with a series of frescoes by several painters, among which the Umbrian Tiberio d'Assisi, depicting the early Franciscan community and the first saints of the order, the miracle of the roses and the concession of the indulgence.

The first nucleus consisted in a chapel with several caves around, at a height of 791 m on the slopes of the Mount Subasio in a splendid ilex-wood.
St. Francis and his disciples retired here for their prayers and meditations.
In 1400 St. Bernardine of Siena erected a small convent and the church of S. Maria delle Carceri, which enlarged and incorporated the previous chapel.
Next to it is located the Cave of St. Francis.
You may take a suggestive walk through the ilex-wood along the caves of the hermits.

Already mentioned in 970, the actual Romanesque-Gothic Benedictine church dates back to the 13th century and is contemporary of the Basilica of St. Francis.
As a matter of fact, Pope Innocent IV consecrated it in 1254, together with St. Francis and St. Rufinus.
Pillars and a cornice divide the front into two orders of three rectangular panels each: three rose-windows correspond to the three portals below. Originally, as all Benedictine churches, the front ended with a tympanon, subsequently demolished after the damages due to an earthquake in the 19th century.
The interior has three aisles, a short transept and originally three apses. The central nave, not having any windows, is lightened exclusively by the central rose-window. The ceiling of the nave is made of wooden beams, while the aisles have flat barrel vaults.
Five stairs lead to the barrel-vaulted transept under which lies the crypt. The central apse is semicircular, the left rectangular, while the right has been walled. On the inner wall of the front and along the sides of the presbitery, Gothic sepulchral monuments of the 14th century. In the left arm of the transept opens a chapel of the 14th century with frescoes of the same period.

Construction work on the church and adjacent convent of St Claire began in 1257, three years after the saint's death and a year after she was canonised.
Until then the sisters of St Claire had lodged at San Damiano. The church dedicated to St Claire occupied the site of the church of San Giorgio, where St Francis had been buried before his remains were moved to the basilica in 1230.
The exterior of the building makes use of alternate strips of pink and white stone, with massive supporting arches either side.
The interior has the same layout as the Upper Basilica of St Francis, with a single nave that terminates in a transept and polygonal apse. Like St Francis', a gallery runs the entire perimeter of the church, although here it is on the same level as the capitols. On the right hand side of the nave the Cappella del Crocifisso and the Cappella del Sacramento were once part of the nave of the previously existing church of San Giorgio, where Pope Gregory IX canonised St Francis in 1228.
The wooden "Crucifix“ in the Cappella del Crocifisso is alleged to have spoken to St Francis in San Damiano, ordering him to repair the church. Relics of St Francis and St Claire are kept behind the grate. The following chapel contains a fresco by Puccio Capanna (1340-46): "Enthroned Madonna and Child with St Claire, St John the Baptist, the Archangel Michael and St Francis", as well as other frescoes of the school of Giotto and Lorenzetti.
The right hand transept contains a panel with the "Life of St Claire“, by the so-called Maestro di Santa Chiara (late 13th century), as well as frescoes depicting St Claire and Biblical scenes by an artist known as the Maestro Espressionista di Santa Chiara (first half of the 14th century). The "Crucifix“ in the apse has also been attributed to the Maestro di Santa Chiara (1280-90).
A colonnade of 12 polygonal columns carved by a local workman in the 15th century encloses the high altar. The wrought iron dividing curtain is 17th century. A detached 14th century fresco of the "Nativity“ displays influences of Giotto in the left hand transept.
The Byzantine style Hodegetria type panel on the left hand wall depicts the "Madonna and Child“ and is by an unknown artist from the 13th century. The lunettes are decorated with scenes from the Old Testament similar to those in the upper cycle of the Upper Basilica of St Francis (late 13th century).
The crypt was built between 1850 and 1872. Restored in neo-gothic style in 1935, it houses the body of St Claire, disovered in 1850.

The Cathedral of San Rufino (St. Rufinus) is a major church in Assisi, Italy, that has been important in the history of the Franciscan order. In this church St Francis (1182) and St. Clare (1193) and many of their original disciples were baptised. When hearing Francis preaching in this church in 1209, Clare of Assisi became deeply touched by his message and she realized her calling. Once St Francis was witnessed praying in this church while, at the same time, he was seen jumping on a chariot of fire in the Porziuncola (as related by Tommaso da Celano, Vita I, chap. XVIII)
This stately church in Umbrian Romanesque style was the third church built on the same site to contain the remains of bishop Rufino, martyred in the 3th century. The construction was started in 1140 according to the designs by Giovanni da Gubbio, as attested by the wall inscription visible inside the apse. He may be the same Giovanni who designed rose-window on the façade of Santa Maria Maggiore (Assisi) in 1163. In 1228, while he was in Asssisi for the canonization of Saint Francis, Pope Gregory IX consecrated the high altar. Pope Innocent IV then inaugurated the finished church in 1253.
The Romanesque façade was built with stones from the Mount Subasio. It is a typical example of the style found in churches of Umbria in the 12th century. This façade is divided in three sections.
-The rather bare top level is triangular with an empty semi-circular arch in the middle, probably meant to contain a frieze or a mosaic.
-The middle level is divided by two vertical pilasters, in line with the arch in the upper level. Each section in this level contains a rose window, but the central one is the largest and the most ornate. It looks as if it is supported by three telamones, themselves each standing on an animal. In the four corners of an imaginary square around the rose window are the four animals, symbols of the four evangelistst.
-The lower level consists of a number of squares and three decorated stone portals with gryphons at the base of the side portals. Especially the middle portal is extensively decorated. In the lunette of the semi-circular arch over the central portal is a relief with the Christ enthroned between the sun and the moon, while on His left is the Virgin, also enthroned, nursing Jesus, and on His right St. Rufinus. The portal is surrounded with three decorated arches with saints, floral and geometrical motifs and intertwined swans. At the base of the middle arch, on each side, is a lion. These sculptures of lions and gryphons have great iconographic importance.
The bottom and the middle part of the square bell tower, on the left side of the façade, were built in the 11th century. It was then situated behind the apse of the previous church built by bishop Ugone in 1029. The top level dates from the 13th century. One can see on the bell tower a colossal one-handed liturgical clock showing the 24 hours of the hora italica (Italian time), a period of time ending with sunset at 24 hours. The foundations of the bell tower rest on a Roman cistern. The structure on the side of the bell tower has been identified as the home of St. Clare.
In 1571 the interior of the cathedral, originally Romanesque in style was completely modified in late Renaissance style by the architect Gian Galeazzo Alessi from Perugia. It consists of a central nave, two aisles, separated by massive pillars, an apse and a dome.
On entering the church, one’s attention is drawn to the baptismal font at the beginning of the right aisle. Here St. Francis was baptised in 1182 and St Clare in 1193, but also many of their original followers and in 1838 Saint Gabriele dell’Addolorata. The font was fashioned from an ancient granite column and is girdled by an iron grating. The terracotta tabernacle was a present in 1882 on the occasion of the 700th anniversary of St Francis birth.
On the right aisle is the Blessed Sacrament Chapel in Baroque style (begun in 1541 and enlarged in 1663), partly frescoed by Giorgetti (1663). The nine wall paintings are attributed to the 17th-century painter Andrea Carloni
The Chapel of Our Lady of Consolation was built in 1496 as a consequence of a miracle. In 1494 people had seen the image of Our lady of Sorrows weeping over the Christ in her arms. This German terracotta sculpture from the early 15th c. has recently been stolen. An identical wooden copy now stands at the same place.
The 19th century main altar stands under the octogonal Renaissance dome over the remains of San Rufino. On both sides stand the marble statues of San Francis and Saint Clare by G. Doupré. In the apse one can admire the majestic choir, with 22 stalls, decorated with wooden carvings by Giovanni di Piertacopo da San Severino (1520). The statue of Saint Rufino of Lemoyne stands at the center of the choir.
There are several paintings by Dono Doni : Christ adored by Saints (1555); on the two altars on both sides of the major one, there are two more works: Deposition (1562) and Crucifixion (1563).
Under the cathedral there is a crypt with the Roman sarcophagus from the 3th century, that once contained the remains of San Rufino. It is frontally sculptured in low relief with the myth of Diana and Endymion. Here one can equally find the Pozzo della Mensa, a medieval well and the ruins of a Carolingian cloister from the 10th century.
The Museo del Duomo exhibits frescoes from the 13th century, reliquaries, and illuminated manuscripts. Its most famous work of art is the triptych Madonna with Child and Saints by Nicolò Alunno (1470).
During restorations of the church in 1969 some of the friezes and stucco work were removed.