The Museum of Human Anatomy in Naples houses a collection of ancient Graeco-Roman crania. The aim of this study was to use multislice computed tomography (MSCT) to evaluate and objectively quantify potential differences in cranial dimensions and shapes between ancient Graeco-Roman crania (n = 36) and modern-day southern Italian crania (n = 35) and then to characterize the cranial changes occurring over more than 2000 years, known as secular change. The authors used traditional metric criteria and morphometric geometry to compare shape differences between the sets of crania. Statistically significant differences in size between the ancient and modern crania included shorter facial length, narrower external palate, smaller minimum cranial breadth, shorter right and left mastoid processes, and wider maximum occipital and nasal breadth. The shape changes from the ancient to modern crania included a global coronal enlargement of the face and cranial diameters, with more anterior projection of the face at the anterior nasal spine, but also posterior projection at the glabella and the nasion. It is not possible to determine whether these differences result exclusively from secular changes in the cranium or from other factors, including a mix of secular change and other unknown factors. To the best of our knowledge, this is the first MSCT-based study to compare ancient Graeco-Roman and modern-day southern Italian crania and to characterize shape and size differences.