Prolonged unloading of bone(s) in the residual limb after amputation may cause significant bone loss in the hip and distal bony end of the residual limb. The purpose of this study was to examine the effect of amputation on bone geometry, volumetric BMD (vBMD), and areal BMD (aBMD) by comparing the intact and residual limbs in unilateral transfemoral and transtibial amputees. Amputees (seven above-knee; seven below-knee) and two groups of nonamputee control subjects gave informed consent to participate in this study. aBMD of the dual proximal femur, lumbar spine, and total body was assessed using DXA. Bone geometry and vBMD were assessed at the distal ends of the residual limb and intact limb and at a comparable cross-sectional slice of the intact limb using pQCT (Stratec XCT 3000). There were no significant group differences in age, height, weight, physical activity, time as an amputee, hours wearing a prosthesis per day, or total body and lumbar spine BMD and BMC. There were significant side x group interactions for total hip, femoral neck, and trochanter BMD, with the amputated side having lower BMD, and differences being most severe in above-knee amputees. Total and cortical vBMD and area were significantly lower at the end of the residual limb compared with the similar slice of the intact limb for both above- and below-knee amputees. In conclusion, amputees exhibited large decrements in BMD, both at the hip and at the end of the residual limb, compared with the intact side. These lower BMD values put amputees, particularly the above-knee amputees, at increased risk for osteoporosis and fragility fractures in the hip.