The article presents a comparative study of change in slice thickness on the accuracy of reconstruction of cranium geometry. Research was performed on 10 different patients. Digital Imaging and Communications in Medicine data were obtained on the Siemens Somatom Sensation Open 40 scanner. At the stage of reconstruction, the same parameters were utilized, while only slice thickness was changed. Modeling with voxel dimensions of 0.4 mm × 0.4 mm × 2.4 mm was chosen as the gold standard over the modeling approach comprising voxel dimensions of 0.4 mm × 0.4 mm × 4.8 mm. The influence of layer thickness on the accuracy of cranium geometry is very similar for the 10 presented patients. The average results show a distribution with a positive skew and kurtosis. The value of skewness is 0.284 (small asymmetry) and kurtosis is 3.746 (a distribution more peaked). Based on 95% confidence, the changes in layer thickness from 2.4 to 4.8 mm generated errors reconstructing the geometry of the cranium by 0.516 mm ± 1.345 mm. The presented research highlights new opportunities to control deviations at the stage of data processing and modeling geometry of the cranium.