The BXD recombinant inbred (RI) strain mice are well-characterized with a wide variety of published metabolic and skeletal phenotypes, as well as gene expression data. We perform a quantitative genetic analysis of femur, tibia, humerus, and ulna lengths in a set of 850 BXD mice of both sexes. Quantitative trait loci (QTL) and strain-by-sex interactions are identified for these traits. We also assess association between these identified QTL and published BXD QTL with effects on other skeletal traits. Additionally, we compare the genetic architecture of long bone traits in the BXD RI strains to the genetic architecture of these traits in other murine crosses to investigate intraspecies variation in genetic effects.