The mechanical integrity of bone is dependent on the bone matrix, which is believed to account for the plastic deformation of the tissue, and the mineral, which is believed to account for the elastic deformation. The validity of this model is shown in this study based on analysis of the bones of vitamin B6-deficient and vitamin B6-replete chick bones. In this model, when B6-deficient and control animals are compared, vitamin B6 deficiency has no effect on the mineral content or composition of cortical bone as measured by ash weight (63 ± 6 vs. 58 ± 3);​ mineral to matrix ratio of the FTIR spectra (4.2 ± 0.6 vs. 4.5 ± 0.2), line-broadening analyses of the X-ray diffraction 002 peak (β002 = 0.50 ± 0.1 vs. 0.49 ± 0.01), or other features of the infrared spectra. In contrast, collagen was significantly more extractable from vitamin B6 deficient chick bones (20 ± 2 % of total hydroxyproline extracted vs. 10 ± 3% p ≤ 0.001). The B6-deficient bones also contained an increased amount of the reducible cross-links DHLNL, dehydro-dihydroxylysinonorleucine, (1.03 ± 0.07 vs. 0.84 ± 0.13 p < 0.001);​ and a nonsignificant increase in HLNL, dehydrohydroxylysinonorleucine, (0.51 ± 0.03 vs. 0.43 ± 0.03, p ≤ 0.10). There were no significant changes in bone length, bone diameter, or area moment of inertia. In four-point bending, no significant changes in elastic modulus, stiffness, offset yield deflection, or fracture deflection were detected. However, fracture load in the B6-deficient animals was decreased from 203 ± 35 MPa to 151 ± 23 MPa, p ≤ 0.01, and offset yield load was decreased from 165 ± 9 MPa to 125 ± 14 MPa, p ≤ 0.05. Since earlier histomorphometric studies had demonstrated that the B6-deficient bones were osteopenic, these data suggest that although proper cortical bone mineralization occurred, the alterations of the collagen resulted in changes to bone mechanical performance.