In this study, we present ongoing research documenting the diversity of European and Hispanic populations. A sample of 1199 crania representing two large geographic and demographically heterogeneous regions (Central and South Europe and Brazil) was tested against a sizable database incorporated into the previous version of 3D-ID software. Craniofacial morphology was described by 3D spatial data processed by methods of geometric morphometrics. The results illustrate morphological complexity and specificity of the examined geographic regions. It also supports the needs to re-evaluate traditional classification systems used in the assessment of ancestry.