THE NAVE
The church has a basilical plant, but with the presbytery of the former basilica highly elevated (see the 1744 plan in pict.1), with three naves divided by two rows of seven columns of different materials and origins, datable around I-II century and perhaps partially coming from the porch of the ancient Aesculapius temple (pict.2); the bases of the columns are the original ones while the stucco capitals date back to the century XVIII restoration. The lacunar ceiling dates 1624 but restored by the pope Pius IX in 1865 (pict.3); the three larger panels have been painted by friar Bonaventura Loffredo: in the middle one "St.Bartholomew refuses to adore the pagan idols". The original cosmatesco floor has been lost during the restorations in century XVIII and has been completely remade in century XIX.

At the left of the entrance one can be recognize the remaining structures of the bell tower base; in 1625, when the façade was moved forward, two sides of the base of the bell tower were opened to form the initial part of the left nave.
In each nave there are three chapels, none of which have remarkable works of art: many paintings have been deeply altered and often damaged by the Tiber floodings.
Starting from the left nave one can see: the Chapel of St.Antonius from Padua, at first decorated by Antonio Caracci but subsequently altered in century XIX; the Chapel of Our Lady of Peace, perhaps the first work of a still inexperienced Antonio Caracci, performed in 1609-10 for order of the cardinal Tonti; the Chapel of the Passion or Crucifix Jesus, in a very bad state, also decorated by Caracci in 1610-11.
In the right nave, in order: the Chapel of St.Francesca Romana, born and lived in the neighbour of the basilica; the Chapel of St.Carlo Borromeo, the last work of Caracci in the basilica (1612-14); the Chapel of St.Francis of Assisi, originally dedicated to St.Bonaventura.

THE TRANSEPT
In the middle of the stairs leading to the presbytery there is the most remarkable element of the church: the well-curb constituting the ideal link to the ancient Aesculapius temple. (pict.4) For a detailed description refer to the section In detail.
The main altar in white marble, gift of the pope Pius IX (see section The history), is supported by a red porphyry basin with a lion shaped prothom, relief handles and a cartouche with the inscription "CORPUS SANCTI BARTHOLOMAEI APOSTOLI" [Body of the saint Bartholomew] testifying the presence of the St.Bartholomew relics (pict.5). Two fragments of the old cosmatesco floor are still inserted in the floor. In the apse is represented the "St.Bartholomew martyrdom" by Francesco Manno (1806) who performed also the architectural restoration of the apse, while the "Crhist in glory and saints" in the apse basin and the other frescoes are by Bonaventura Loffredo.

In the right side of the transept two Romanic stilofori [column supporting] lions (century XII) probably previously placed at the entrance of the ancient church (pict.6-7), lead to the chapel of the Virgo or of the Holy Sacrament, also known as Chapel Orsini di Pitigliano, from the family that assumed its patronage in the XVII century; the axis of the chapel, not corresponding to the basilica one, could date back its origin to the ancient basilical building. The ceiling is attributed to Martino Longhi the Older (1601). Above the frontal of the altar decorated with polychrome marbles (pict.8) and keeping the St.Teodora's relics (as indicated by the inscription "HIC IACET CORPUS BEATÆ THEODORÆ MATRONÆ ROMANÆ" [here lies the body of the blessed roman matron Teodora]), there is an ancient fresco (end of century XIII) found out in 1904 and representing the "Virgo on the throne with the blessing Infant Jesus and saints" (pict.9).
In the left wall of the chapel it is set a cannon ball fallen into the church during the clashes in 1849; more information are in the section In detail.
On the right wall of the transept, before entering the chapel, a round brass basin of Arab make is kept behind an iron grating (century X-XI) (pict.10). According to the tradition it was the container, or its cover, used to collect the St.Bartholomew relics during their transport from Benevento to Rome.
In the left side of the transept there is the old sacristy which became a chapel due to Julius III (middle of century XVI); it was dedicated at first to St.Paolino from Nola, represented "in glory" (1704) in the middle of the vault, and at present to St.Adalberto. Above the altar, below a XVII century Annunciation, there is a painting (pict.11) representing the "Assunta with saints Paolino, Adalbert, Esuperanzio e Marcellus" (1665); their relics, with the exception of the St.Paolino ones moved to Nola in 1909, are still kept in the chapel. The chapel constituted up to 1846 the see of the Millers Brotherhood under the protection of St.Paolino and is decorated with images relevant to their activity shown in the section In detail. A plaque on the left wall commemorates a restoration carried out in 1626.
A door on the right wall leads to the present sacristy.

THE CRYPT
From the little garden at the left side of the church it is possible to come down to the crypt, originally accessible from the church nave through two flights of stairs. In the crypt, collapsed during the 1557 flooding together the upper apse, and whose restoring has been completed in 1975, it can be recognized the ancient plant of the church with small naves and cross-vaults supported by two rows of three small columns; two capitals, original from the ancient basilica, are decorated with the imperial crowned eagle (pict.12) symbol of Otto III. In a small room there are a roman tombstone, used as architrave, and two eighteenth-century grave stones (pict.13).