Fragility fractures affect individuals of all ages and result in tremendous financial cost for both the individual and the medical community. Although BMD is a powerful clinical tool, a familial history of fracture is still the best predictor of an individual's fracture risk. Traits describing the morphology and quality of bone are known to be heritable, but the precise genetic mechanisms responsible for this variation, and their connection to whole bone functionality, remain unclear within species. To determine the genetic basis for intra-species variation in skeletal mechanical function, we used inbred mice as models for bone mechanical function in humans. FTIRI spectroscopy revealed significant variation in mineral composition and matrix maturity among inbred mice and this variation was associated with differing tissue-level mechanical properties as measured by micromechanical testing in tension. Mice with more slender bones had more mineral packed into their bones and their bone tissue had larger moduli (tissue-level stiffness). Thus, intra-species genetic variation results in significant tissue-level differences in quality and mechanical functionality, all of which contribute to whole bone functionality. A phenotypic analysis of chromosome substitution strain mice revealed that expected relationships among bone quality and morphological traits can be disrupted by single chromosome perturbations. Not only could a large bone (B6 femora) be shifted to a slender (A/J femora) phenotype, but also many substitutions created phenotypes that were even larger than B6. Concurrent with these changes were changes in mechanical properties;​ femora with increased and decreased mechanical properties resulted from single chromosome substitutions. Thus, multiple genes appear to play a role in the co-variation of traits in mouse femora. Consequently, genetic regulation of bone functionality and fracture risk within species likely arises from multiple gene interactions coordinately directing the cellular control of 1) tissue-level mineral and matrix deposition and 2) whole bone size and shape. These findings provide new insight into fracture susceptibility in humans and open up potential avenues for better prediction and treatment of fragility fractures.