The primary purpose of these studies was to determine if men with spinal cord injury (SCI) have lower trabecular bone microarchitecture about the knee and impaired bone geometric structure and strength in the mid-thigh relative to controls. A secondary purpose was to assess the degree of muscle atrophy using magnetic resonance imaging and dual-energy X-ray absorptiometry. Magnetic resonance images were used to assess bone in the lower limbs, and to quantify skeletal muscle mass in the mid-thigh. Dualenergy X-ray absorptiometry was used to quantify fat-free soft tissue mass (FFST) in the mid-thigh. The distal femur and proximal tibia of men with SCI had fewer trabeculae (21 and 19 %) that were further apart (43 and 32 %) than controls, resulting in less bone per unit volume after injury (26 and 18 %). In addition, within a small area of the proximal tibia (~3 cm), the volume and number of trabeculae decreased from the most proximal end to the most distal end in the SCI group than controls while the opposite was the case for spacing. Differences in microarchitecture between groups along the length of the femur, in contrast, were consistent. Total volume of the mid-femur was not different and total width only modestly thinner (3 to 6%) in the SCI group than controls, but cortical volume and width were 22 to 39 % less in the SCI group. The cortical wall was particularly thin and the endosteum particularly thick in the posterior region. Congruent with the structural deterioration, bone strength was reduced by 15 to 35 %. With respect to skeletal muscle, the SCI group had lower muscle mass (45 %) and FFST (38 %) in the mid-thigh than controls; however, skeletal muscle was disproportionately lower, as indicated by the lower proportion of muscle in the FFST of the SCI group (80 % vs 91 %, respectively; P < 0.05). Despite the latter discrepancy, strong relationships were observed between mid-thigh skeletal muscle and FFST in the SCI men and controls (r = 0.99 and 0.96, respectively; P < 0.05). These studies suggest that trabecular bone microarchitecture and bone geometric structure deteriorates to a great extent in the lower limbs after SCI. Moreover, they suggest that SCI results in a disproportionately lower concentration of skeletal muscle in the FFST.