Bone quality, a contributor to bone strength, is determined by structural and mechanical properties, which may be analyzed by gross and/or microscopic methods. Variables that contribute to bone quality, such as porosity, can provide insight into the health and lifestyles of people in prehistory. This study tests the ability of microcomputed tomography (µCT) to capture and characterize cortical canal systems in archaeological bone. Seven variables and 71 femora are analyzed to explore bone dynamics in prehistoric foragers from Lake Baikal, Siberia. The results indicate that canal number and canal separation differ significantly (P < 0.05) between age‐at‐death categories, but only for the pooled and male samples. When merged into a new variable by means of principal components analysis, canal diameter and canal surface to canal volume are also able to discriminate amongst age‐at‐death categories, as well as between the sexes. However, the overall lack of significant differences between the sexes and amongst age‐at‐death categories indicates that Baikal forager bone quality (i.e., canal architecture) did not change drastically throughout the lifespan. Interestingly, principal component one identified an untested variable that contributes to canal microstructure variability, and a sexual division of labor may promote divergent trends in canal degree of anisotropy between the sexes. Overall, µCT provides an alternate method for exploring bone quality in archaeological remains, complementing existing methods such as thin‐sectioning and gross morphological analyses. Am J Phys Anthropol, 2014. © 2014 Wiley Periodicals, Inc.