Here, we apply geometric-morphometric shape analysis to Middle Paleolithic bone retouchers from Chagyrskaya Cave in the Altai Mountains of southern Siberia. The cave contains evidence of the easternmost manifestation of the Micoquian industry, associated with Neanderthals at end of MIS4 and the beginning of MIS3. Taphonomic and scar pattern analyses were performed first on random samples exhibiting appropriate characteristics. Several retouchers produced on intentionally modified blanks were identified in our sample, suggesting that some of the Chagyrskaya Cave bone retouchers can be described as formal tools. All retouchers from Chagyrskaya Cave exhibit a similar general morphology. The most variable group is comprised of complete retouchers without blank modifications. Retouchers exhibiting minor damage affect the general pattern of variability and it is not possible to identify them only by means of geometric-morphometric shape analysis. Complete retouchers with blank modifications fall within the range of variability of complete retouchers without blank modification, suggesting intentional shaping of blanks to conform to a standard template. The range of variability of the bone retouchers does not differ significantly from that of the most highly modified lithic artifacts at Chagyrskaya – plano-convex bifaces – which may indicate intentional shape control for such artifacts. Geometric-morphometric analysis indicates that the anatomical origin of bone blanks does not significantly influence the retouchers’ shape, which may point to strict blank selection and, at the same time, intentional modification. Our results raise questions regarding the integration of retouchers into a complex, multidimensional “chaine-opératoire” as well as the nature of Neanderthal cognitive abilities. Geometric-morphometric shape analysis represents a major step forward in the study of prehistoric retouchers.