Inter-population variation of cranial morphology, which plays an important role in human evolution studies and biological research, can be studied morphologically and metrically. Geometric morphometry compares body forms using specific landmarks determined by anatomical prominences. The aim of this study was to identify cranial shape differences between the crania of Byzantium period humans and modern humans. Variability in cranial shape was examined using the geometric morphometric technique based on landmark coordinates. Landmark coordinate data were collected from two-dimensional digital photogrammetry and were analyzed using generalized Procrustes analysis, hierarchical clustering and thin-plate spline analysis.