Location: The Roman Forum (See maps below).
The church is the site where, according to tradition, the apostles Peter and Paul were incarcerated for nine months before their martyrdoms.  It claims an ancient and illustrious foundation by Pope Sylvester I (reigned 314–335), the pontiff who baptized the first Christian emperor, Constantine the Great (reigned 307–333), who, in turn, granted substantial privileges to the Roman church. According to the legend transmitted via early modern sources, after a visit to the site Constantine recommended that the pontiff consecrate a church there.  The church then became an important pilgrimage destination because of its connection with the two apostles. In the early modern period, structural modifications to the site were made for Jubilee years, when pilgrims flocked to Rome. Despite drastic changes throughout the city over the centuries, the Church of San Pietro in Carcere maintained a privileged status as an important locus of early Christianity.
From an urban perspective, the church had only a marginal location in the early modern period, but the site, at the foot of the hill across from the Capitoline facing the Arch of Septimius Severus, had been at the center of civic life in ancient Roman times. The famous statue of Marforius, which once stood near the church, gave its name to the adjacent street. The church was a two-level subterranean structure with an irregular plan, atypical for a church; it reflected the inherited structure of the prison. The ancient prison had been carved into the hill near the Campidoglio, behind the Church of Santa Maria in Aracoeli, and had a ground-level component that would subsequently disappear.  Pompeo Ugonio (1588), Ottavio Panciroli (1600), and Pompilio Totti (1630) report that the more ancient space would have been the upper level of the prison, the lower one being excavated two regimes later.  In fact, the lower level is datable to approximately the seventh‒sixth century BCE and the upper level to the republican period.  The prison was also called the Carcer Tullianum, either from the Roman king Servius Tullius, who added the lower level of the prison, or from a spring (tullius in Latin) present in that space.  Early modern sources refer to the prison either as Tulliano, according to ancient custom, or Mamertino, following period custom.  The latter appellation supposedly derived either from the ancient Roman king Ancus Marcius or from the name of a prefect of Rome of an unspecified time. 
Each level played a different role in ecclesiastical practices at the site. The upper level was associated with an image of Saint Peter that, according to legend, resulted from an imprint made when the saint hit his head against a wall as he was pushed down the stairs. It was supposedly worn to the point of illegibility from longstanding veneration by believers, which included touching it. The portion of wall bearing its traces was removed to create a door for easy access to the site for the Jubilee of 1600.  Totti called the carpenters “ignorant” for taking such reckless action. Practical issues such as topography and accessibility and technical details such as thickness of the wall must be considered in any discussion of whether they were unaware of the image or made a conscious decision. It is known, however, that around 1597 the carpenters were rebuilding the Church of San Giuseppe dei Falegnami on top of the Church of San Pietro in Carcere. While we lack visual evidence for this specific moment, we can imagine the site obstructed by scaffolding and littered with materials. Confronted with the necessity of making the site accessible to pilgrims, the carpenters may have opted for the solution that promised the least interference with construction. The removal was supposedly redressed in the early eighteenth century when an image, alleged to be the portion of the wall bearing the impression, was placed behind a protective grille in the upper chamber of the old prison. 
The lower level of the Church of San Pietro in Carcere was linked to a miracle performed by the two apostles while incarcerated there: the emergence of a spring.  Seventeenth-century sources questioned the authenticity of the fountain then at the site because various buildings and fountains had over centuries come to light in the area of the Campidoglio.  In the same underground space was preserved the column to which the two apostles had been chained. Later this space came to be called the Carcer Tullianum, whereas the upper space was considered the Church of San Pietro proper.  Early modern sources, however, conceived of the two levels as a unit constituting the Church of San Pietro in Carcere. 
Early modern depictions of the church are rare. Contemporary maps showed buildings only at surface level. In an illustration included in Pietro Martire Felini’s Trattato (1610), the Church of San Pietro in Carcere appears clearly distinguished from that superimposed on it (San Giuseppe dei Falegnami, recently completed in 1602).  The structure of San Pietro protrudes, creating a platform in front of the facade of the Church of San Giuseppe. The construction materials are evidently different, the masonry of San Pietro in Carcere being made of rougher materials. The entrance to the lower church is delineated by a large doorframe. Two flights of stairs offer access between the two churches. The epigraph inscribed on the occasion of the restoration of the stairs for the Jubilee of 1625 claims that the space of the Church of San Pietro had remained intact. 
The dedication of the church changed to Saint Peter, Saint Paul, and Saint Joseph after the carpenters succeeded in 1540 in securing the site from the rector (rettore) of the nearby Church of Santa Martina, under whose jurisdiction the Church of San Pietro in Carcere resided at the time.  When the carpenters decided to build a separate and elaborate structure above the church, the dedication of the ancient church was restored to Saint Peter and Saint Paul, whereas the upper church was dedicated to Saint Joseph, the patron saint of the carpenters. When the artists moved into the nearby Church of Santa Martina in 1588, the Archiconfraternita di San Giuseppe had been at the Church of San Pietro in Carcere for almost half a century, during which time they had built a church on top of it. Interactions between the Accademia di San Luca and the carpenters concerned jurisdiction over the site. Discussions involved the leaders of the Archiconfraternita, but San Pietro in Carcere occasionally surfaces in the Accademia’s documents as well.  In some cases, they refer to the site in relation to earlier transactions when San Pietro in Carcere was first known as such. 
-- Silvia Tita