The Basilica of SS. Giovanni e Paolo stands over a complex comprising several Roman houses of different periods. According to tradition, this was the dwelling of John and Paul, both of whom, having suffered martyrdom by execution were buried on the site of their own house (362 AD). During the third century AD, these different properties were combined under a single owner and transformed into an elegant pagan house characterised by finely-decorated rooms. 

At the beginning of the fourth century AD the house became a meeting place for the Christian community of the area and at the end of the same century it became a sanctuary and here the believers came and venerated the tombs of the martyrs. Some parts of the building were altered to the needs of the cult and a new room was created: it had a small window (fenestrella confessionis) and from here the faithful could see the tombs of the martyrs. 

The walls of this room were decorated with a cycle of frescos dating back to the mid-fourth century. In the fourth century the church was built: the upper floors of the house were destroyed and the ground floor filled in, thus allowing the rooms to be preserved.