Down syndrome (trisomy 21) is associated with reduced bone density in humans, but it is unclear whether this is due to specific effects of chromosome 21 genes or lifestyle factors. Mouse models with aneuploidy of segments of mouse chromosome 16 that are homologous to human chromosome 21 can be used to elucidate the mechanism by which Down syndrome phenotypes arise. Ts1Rhr and Ms1Rhr mice are trisomic and monosomic, respectively, for the hypothesized "Down syndrome critical region" containing approximately 33 genes. We assessed the skeletons of these mice from 3 to 16 weeks of age using dual X-ray absorptiometry. Ts1Rhr mice were unexpectedly similar to normal controls, showing that a larger region of trisomy is necessary to recapitulate the Down syndrome phenotype. Ms1Rhr mice, in contrast, showed decreases in weight, bone mineral content, bone mineral density, and bone area from weaning to adulthood. Regional bone density was also decreased in the femur, tibia, and lower lumbar spine. The microarchitecture of 3 week old Ms1Rhr femurs was then analyzed using µCT. Volumetric density, total tissue volume, bone volume, and bone fraction were all reduced in both cortical and trabecular bone. Ms1Rhr trabeculae were thinner and had decreased connectivity. A 31.5% reduction in the level of insulin-like growth factor I in the serum was found, and we hypothesize that this is responsible for the bone density phenotype. We discuss bone-related genes in the region and propose that humans with distal chromosome 21 deletions may exhibit reduced bone density.