The church was one of the tituli, the first parish churches of Rome. It was probably built in the 4th century under Pope Silvester I (314–335), rebuilt in the 12th century by John of Crema, and again by Giovanni Battista Soria, funded by Scipione Borghese, in the early 17th century.
The area beneath the sacristy was investigated by Fr. L. Manfredini and Fr. C. Piccolini in 1907. They found remains of the first church (see below). After they had made this discovery, the area was excavated and studied.
List of Ordinaries 
- Cardinal-Priest Fabrizio Spada (23 May 1689 - 30 April 1708), elevated to Cardinal-Priest of Santa Prassede
- Cardinal-Priest Filippo Antonio Gualterio (30 April 1708 - 29 January 1724), elevated to Cardinal-Priest of Santa Cecilia in Trastevere
- Cardinal-Priest Prospero Marefoschi (29 January 1725 - 19 November 1725), elevated to Cardinal-Priest of San Callisto
- Cardinal-Priest Giulio Alberoni (20 September 1728 - 29 August 1740), elevated to Cardinal-Priest of San Lorenzo in Lucina
- Cardinal-Priest Sigismund von Kollonitsch (29 August 1740 - 12 April 1751)
- Cardinal-Priest Giovanni Giacomo Millo (10 December 1753 - 16 November 1757)
- Cardinal-Priest Giovanni Battista Rovero (2 August 1758 - 9 October 1766)
- Cardinal-Priest Filippo Maria Pirelli (1 December 1766 - 10 January 1771)
- Cardinal-Priest Francesco Maria Banditi (18 December 1775 – 27 January 1796)
- Cardinal-Priest Vincenzo Gioacchino Raffaele Luigi Pecci (22 December 1853 – 20 February 1878), elevated to Papacy
- Cardinal-Priest Friedrich Egon von Fürstenberg (27 February 1880 – 20 August 1892)
- Cardinal-Priest Philipp Krementz (19 January 1893 – 6 May 1899)
- Cardinal-Priest Francesco di Paola Cassetta (22 June 1899 – 27 March 1905), elevated to Cardinal-Bishop of Sabina
- Cardinal-Priest Pietro Maffi (18 April 1907 – 17 March 1931)
- Cardinal-Priest Theodor Innitzer (13 March 1933 – 9 October 1955)
- Cardinal-Priest Antonio María Barbieri (15 December 1958 – 6 July 1979)
- Cardinal-Priest Bernard Yago (2 February 1993 – 5 October 1997)
- Cardinal-Priest Paul Shan Kuo-hsi (21 February 1998 – 22 August 2012)
Art and architecture 
The belltower dates from the 12th century rebuilding. The interior of the church was rebuilt in the 1620s on the site of a 12th-century church. The 22 granite columns in the nave are recycled antique columns. The floor is Cosmatesque, but most of it is hidden by the pews. The confessio in the sanctuary area is from the 8th century. The high altar is from 1127, with a baldachino from (1627 or 1641) by Gian Lorenzo Bernini.
The painting in the middle of the Baroque coffered ceiling is by Guercino, and depicts the Glory of Saint Chrysogonus. Likely a copy, in which case the original was taken to London, but it might also be vice versa.
On the left side of the nave is the shrine of Blessed Anna Maria Taigi. She was buried here in the habit of a tertiary of the Trinitarians. See some of her belongings are in the adjacent monastery, where they are kept as relics.
The monument at the left of the entrance, dedicated to cardinal Giovanno Jacopo Millo was completed by Carlo Marchionni and Pietro Bracci. Along the right nave are the fresco remains, including a Santa Francesca Romana and a Crucifixion, attributed to Paolo Guidotti and transferred from the church of Saints Barbara and Catherine. The nave also contains a painting of Three archangels by Giovanni da San Giovanni. The nave has a Trinity and Angels by Giacinto Gimignani, while the altar has a Guardian Angel by Ludovico Gimignani. The presbitery and ciborium are surrounded by four alabaster columns, it is a work by Soria. The apse has frescoes of the Life of Saint Crisogono (16th century) and below Madonna & child with saints Crisogono & James by the 12th century school of Pietro Cavallini. The presbitery vault is frescoed with a Virgin by Giuseppe Cesari.
Remains from the first church, possible from the reign of Constantine I, and earlier Roman houses can be seen in the lower parts, reached by a staircase in the sacristy. The ruins are confusing, but you can easily find the apse of the old church and you can see the remains of the martyr's shrine in middle of the apse wall. The church had an uncommon form; rather than the normal basilical plan with a central nave and two aisles on the sides, it has a single nave.
On either side of the apse are rooms known as pastophoria, service rooms of a type uncommon in the West but normal in Eastern churches. The one on the right-hand side is though to have been used as a diaconium, with functions resembling those of the sacristy in later churches. The other would then probably have been a protesis, where holy relics were kept.
A number of basins were found here during the excavations, including one cut into the south wall. As the plan is so atypical of early Roman churches, some believe that the structure originally had a different function, and the presence of the basins could mean that it was a fullonica, a laundry and dye-house. The area was a commercial district at the time, so this is quite likely. Others think that the basin in the south wall was made for baptism by immersion. As there were other basins too, it seems more likely that it was originally intended for a different use, but it may very well have been used as a baptismal font after the building had been consecrated as a church.
Several sarcophagi have been preserved here, some beautifully decorated.
Below the first church are remains of late Republican houses.
The feast day of St Chrysogonus, 24 November, is also the dedication day of the church. Pilgrims and other faithful who attend Mass on this day receive a plenary indulgence.
Cigola Michela, "La basilica di s. Crisogono in ROma. Un rilievo critico", numero monografico del Bollettino del Centro di Studi per la Storia dell'Architettura, n. 35, Roma, dicembre 1989, link at 
Media related to San Crisogono at Wikimedia Commons