The museum includes artefacts dating from prehistoric periods of up to the greek and Roman excavations from the city and from other sites in Sicily.

The ground floor is divided into 3 sectors (ABC), while the main building (Area 1) is dedicated to the history of the museum and there are briefly presented the materials exposed in individual sectors.

The Area A, dedicated to prehistory (upper-Paleolithic Age of Iron), with an exhibition of rocks and fossils testify that the various forms of animal in the Quaternary. It is preceded by a section which shows the geological characteristics of the Mediterranean and the area Iblea.

In the area B, dedicated to the Greek colonies in Sicily period of Ionic and Doric, you can identify the location of Greek colonies in Sicily and their city of origin. They are also exposed: a marble statue of Kouros acefala from Leontinoi (Lentini) dated in the early fifth century BC The findings of Doric colony of Megara Hyblaea, votive statues of Demeter and Kore and a Gorgone, a head of Augustus from Centuripe. It is also exposed the Venus Anadiomene also known as Venus Landolina dall'archeologo that discovered in Syracuse in 1804, defined wonderful "for the excellence of modeled, the exquisite treatment of naked, incredible liveliness and morbidity" from Bernabò Brea.

In Area C are exposed findings of sub-colonies of Syracuse: Akrai (664 BC), Kasmenai (644 BC), Camarina (598 BC), Eloro. Also findings from other towns of eastern Sicily and Gela and Agrigento.

The sector D, place on the first floor, was inaugurated in 2006 and contains artefacts dating back to Hellenistic-Roman. Inside are contained some of the most famous exhibits of the museum: the Venus Landolina and Sarcophagus of Adelfia, as well as a selection of coins from the Cabinet numismatic square Duomo.