X-ray Computed Tomography (X-ray CT) is a sophisticated non-destructive imaging technique to investigate structures and materials of complex objects, and its application can answer many conservation and restoration questions. However, for Cultural Heritage investigations, medical CT scanners are not optimized for many case-studies: These instruments are designed for the human body, are not flexible and are difficult to use in situ. To overcome these limitations and to safely investigate works of art on site—in a restoration laboratory or in a museum—the X-ray Tomography Laboratory of the University of Bologna designed several CT systems. Here we present two of these facilities and the results of important measurement campaigns performed in situ. The first instrument, light and flexible, is designed to investigate medium-size objects with a resolution of a few tens of microns and was used for the CT analysis of several Japanese theater masks belonging to the collection of the “L. Pigorini” Museum (Rome). The second is designed to analyze larger objects, up to 200 cm and was used to investigate the collection of the so-called “Statue Vestite” (devotional dressed statues) of the Diocesan Museum of Massa.