A free commune was founded in Cagli at the end of the 12th century, and it quickly subdued more than 52 surrounding castles, overthrowing the rural lords and threatening the feudal powers of the abbots.

When the city was partially destroyed by fire, started by Ghibelline factions in 1287, the settlement was moved down from the slopes of Monte Petrano and rebuilt anew on flatter land, incorporating the pre-existing suburb.

The economic development of the city centred mainly on the manufacture of woollen cloth (later also silk) and the tanning of hides, industries that grew considerably under the dukes of Urbino.

When the Duchy of Urbino was handed over to the Papal States in 1631, Cagli became subject to the same economic policies as the rest of the Marche region, principally cereal cultivation.

The railway line was destroyed by Nazi forces in 1944 and the Via Flaminia lost its importance as a major road, marking a long period of decline for Cagli and the surrounding valleys, which was to be reversed only towards the end of the second Millennium.

The fortifications date back to a time when architects like Francesco di Giorgio Martini were testing out innovative solutions to the problems posed by new developments in artillery.

On the side altars the principal works (counterclockwise from the right) are: two fragments of framed frescoes, once attributed to Antonio Alberti da Ferrara, now attributed to the Secondo Maestro of the Oratory of St John the Baptist, Urbino; the Miracles of the Snow by Ernst van Schayck(1617) and a young Gaetano Lapis (1730); a processional wooden crucifix, from the Northern European school, from the second half of the 15th century; an altarpiece (1540) by Raffaellino del Colle.

The interior was decorated with frescoes, of which several large fragments still remain: the Martyrdom of St Apollinia (1455) is by Jacopo Bedi from nearby Gubbio, while the others have elements that are reminiscent of the Basilica of San Francesco in Assisi.

Made from gilded and lacquered wood with great Solomonic columns, at its centre is the painting depicting Noli me tangere (1504), signed "THIMOTHEI DE VITE URBINAT.

The building, onto which was added the Palazzo del Podestà (the monumental façade overlooks via Alessandri), was donated by the Comune to Federico III da Montefeltro in 1476.

To the side of the undecorated entrance are three standard measuring units: piede (foot), braccio (arm) and canna (cane): to these should be added the stub of a Roman column known as the "Cagliese quarter" now positioned just inside the main room on the ground floor.

The Gothic portal (1424) can still be seen on the left wall; it was sculpted by Maestro Antonio di Cristoforo of Cagli and the 17th century painted decoration is by Lodovico Viviani.

These are (from the left) the funeral monument with a fresco of Christ in the Tomb between Saints Jerome and Bonaventure(1481) and the celebrated Tiranni Chapel, considered to be his masterpiece, which dates from the early 1490s.

Beside the Virgin's throne, the work depicts an angel gazing outwards from the scene; it is traditionally believed that this is a portrait of Raphael as a child, while the face of St John the Baptist appears to be a self-portrait of Santi himself.

About 8 kilometres (5 miles) to the northwest of Cagli and 4 km (2 mi) west of the Via Flaminia, at the modern Acqualagna, is the site of an ancient town; the place is now called piano di Valeria, and is scattered with ruins.