Tradition claims that Saint Hippolytus, following his appointment as Bishop by Pope Callixtus I in the year 221, was later thrown into a well in 229 while celebrating the Holy Communion.
Between the end of the 4th and the beginning of the 5th C. AD a basilica was erected on the site of his martyrdom, over the ruins of buildings dating back to the age of Trajan (a spa and a cistern complex).
The original construction, with a single nave, was subsequently modified.
All that remains of the original structure is the 12th C. Romanesque bell tower which was probably transformed into a watchtower in 1578 by Pope Gregorius XII following a raids by buccaneers along the coast. Among the many valuable marble fragments found in the church, the most remarkable is a rare and beautiful altar tabernacle.