The museum, set up in 1875 in the San Nilo monastery, founded in 1004 on the ruins of a Roman villa, contains material that has been collected over the centuries by the Basilian monks.
The archeological collection includes, other than a famous ancient stone of a dead young man in a sitting position, dating to the end of the fifth/beginning of the sixth century B.C., numerous exhibits in marble, sarcophaguses and portraits including one of Alexander the Great and another of Constantine. There is also an interesting series of inscriptions that are mainly funerary.
The historical-artistic collection is also of great interest, containing frescos from the medieval church, Islamic and Sicilian ceramics, rare, sacred objects and paraments like the precious Omophorion, a bishop’s pallium in woven in silk and gold, from the 14th century.
A reconstruction of the hypogeum known as "delle Ghirlande", a sepulchre from the Imperial Age discovered in 2000 near the Ad Decimum and Grottaferrata catacombs, where the sarcophaguses of Aebutia Quarta and T. Carvilinus Gemellus, father and son respectively, were found, is scheduled to be built in the museum. One of the objects discovered in the grave is a precious ring made in gold and rock crystal.
The museum is closed for renovation.

Galleria fotografica