Abstract: This article is dedicated to the peculiarities of arrangement of altar space in the Franciscan Churches of Umbria during the XIII-XVI centuries. The authors underline the typological and liturgical dependence of the initial layout of Basilica of Saint Francis of Assisi on the structure of apsidal-papal basilicas in Rome (namely St. Peter’s Basilica and Basilica of St John Lateran). The design of the Franciscans’ main basilica affected virtually all churches of the order in Umbria (Perugia, Città di Castello, Todi, Borgo Santo Sepolcro, and other). The choir in these churches was situated in the chancel space of the apse. It is demonstrated that this pattern hinged upon the location of the Pope’s throne along the arc of apse (in St. Peter’s Basilica and Basilica of Saint Francis of Assisi). The preserved original altars of the XIII-XIV centuries in Franciscan churches allow positioning these sites into a single stylistic-typological row, and place into a separate category the mensae altars: wide stone throne surrounded by the ogival arch. The analysis of altar décor allows concluding on the similarity of Franciscan altars with the early-Christian sarcophagi of a colonne type. The authors examine the case of using sarcophagi as a tomb of Saint Giles in the Church of San Francesco al Prato, Perugia. It is highlighted that the structure of altar space and presence of monumental chancel screen tramezzo defined the absence of altar ciborium in the Franciscan churches.