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Microfocus X-ray is a perspective approach to evaluation of bone condition in pathological and destructive processes, which helps to describe small and low-contrasting details of images with magnification and in good quality. We used the method to study inner structure of small tubular bones (mainly, manual phalanges) from representatives of Middle Pleistocene, Upper Palaeolithic and living Homo. Humans with so called “archaic” features originated from 12th level of Denisova Cave, from Okladnikov and Chagyrskaya Caves in highland Altai, from Kiik-Koba shelter in Crimea. At least majority of them were Neanderthals. Anatomically modern humans in our study were presented by mature man Sunghir 1 and modern males in age from 20 to 55 years. In addition to common anatomical criteria, we discovered clear differences between “archaic” and “modern” samples in degree of trabecular system development and mineral density. Although the Upper Palaeolithic Sunghir male shows visible bony change under mechanical load, he remains to be entirely anatomically modern. Our method can be proposed for simple recognizing of “archaic morphology bearers” in fragmentary and strongly destroyed fossil remains.