We examined femora from adult female AXB/BXA recombinant inbred (RI) mouse strains to identify epiphyseal traits that are functionally related and to determine how interactions among these traits contribute to organ-level functionality. The results of this study validated that variation in bone morphology is linked to variation in trabecular architecture and tissue quality. More than 1/3 of the 36 correlations examined were significant, indicating that many bone traits covaried or were functionally related. Path analysis revealed novel interactions between traits defining epiphyseal volume, body weight, trabecular architecture and tissue quality. The causal relationship among these traits suggested a biological adaptation process, which allows for the forgiveness of genetic variation in physical bone traits, so that bone can be flexible in creating functional structures.