Between 2013 and 2015, Arcadia University in partnership with the Pontifical Commission for Sacred Archaeology and the University of Catania undertook new excavation campaigns in the Catacombs of St. Lucy at Siracusa. The research focuses on some very problematic parts of Region C of the complex, including Oratory C, the so-called Pagan Shrine and Crypt VI. These areas document most effectively the long life of this Christian hypogeum, which incorporated previous structures and artefacts related to the Greek period and continued to be used until the Middle Ages. During the excavation an array of 3D digital techniques (3D scanning, 3d Modelling, Image-based 3D modelling) was used for the daily recording of the archaeological units, but also to create high-resolution virtual replicas of certain districts of the catacombs. Furthermore, the same techniques were applied to support the study of certain classes of materials, such as frescoes and marble architectural elements that could otherwise only be studied in the dark environment of the catacombs, making the visual analysis of such complex artifacts difficult and sometimes misleading, not to mention that the frequent use of strong sources of light for study can also endanger them. The virtual archaeology research undertaken at the Catacombs of St. Lucy represents the first systematic application of 3D digital technologies to the study of such a special archaeological context in Sicily.