U unutrašnjosti je [[Brod (arhitektura)|brod]] sa dva prolaza i tri [[Apsida|apside]] rardvojene antičkim [[Dorski red|dorskim]]
The aisles are surmounted by cross-vaults, while the nave has an 18th century [[Coffer|coffered]] [[ceiling]], [[fresco]]ed in the center by [[Giovanni Battista Parodi]], portraying the ''Miracle of the Chains'' (1706).
[[Michelangelo's Moses|Michelangelo's ''Moses'']] (completed in 1515), while originally intended as part of a massive 47-statue, free-standing funeral monument for [[Pope Julius II]], became the centerpiece of the Pope's funeral monument and tomb in this, the church of [[della Rovere family]]. Moses is depicted with horns, connoting "the radiance of the Lord", due to the similarity in the Hebrew words for "beams of light" and "horns". This kind of iconographic symbolism was common in early sacred art, and for an artist horns are easier to sculpt than rays of light.
Other works of art include two canvases of ''Saint Augustine'' and ''St. Margaret'' by [[Guercino]], the monument of [[Cardinal (Catholicism)|Cardinal]] [[Girolamo Agucchi]] designed by [[Domenichino]], who is also the painter of a sacristy fresco depicting the ''Liberation of St. Peter'' (1604). The [[altarpiece]] on the first chapel to the left is a ''[[Deposition from the Cross|Deposition]]'' by [[Cristoforo Roncalli]]. The tomb of Cardinal [[Nicholas of Kues]] (d 1464), with its [[relief]], ''Cardinal Nicholas before St Peter'', is by [[Andrea Bregno]]. Painter and sculptor [[Antonio Pollaiuolo]] is buried at the left side of the entrance. He is the Florentine sculptor who added the figures of [[Romulus and Remus]] to the sculpture of the[Capitoline Wolf on the Capitol. <ref>"Sculpture" . ''The Oxford Encyclopedia of Classical Art and Architecture.'' Ed. John B. Hattendorf. Oxford University Press, 2007.</ref> The tomb of Cardinal Cinzio Passeri Aldobrandini, decorated with imagery of the Grim Reaper, is also in the church.
In 1876 archeologists discovered the tombs of those once believed to be the [[Woman with seven sons|seven Maccabean martyrs]] depicted in 2 Maccabees 7-41.<ref>Taylor Marshall, <em>The Crucified Rabbi: Judaism and the Origins of the Catholic Christianity</em>, Saint John Press, 2009 ISBN 978-0-578-03834-6 page 170.</ref> It is highly unlikely that these are in fact the Jewish martyrs that had offered their lives in Jerusalem. They are remembered each year on 1 August, the same day as the miracle of the fusing of the two chains.
18th century fresco, ''The Miracle of the Chains'' in the center of the coffered ceiling by Giovanni Battista Parodi (1706).|thumb|240px]]
The third altar in the left aisle holds a mosaic of [[Saint Sebastian]] from the seventh century. This mosaic is related to an outbreak of plague in [[Pavia]], in northern Italy. It would only stop if an altar was built for St. Sebastian in the church of S. Pietro in Vincoli in that city. Somehow this story also became accepted in Rome. Hence the altar.