Patients with transfemoral amputation (TFA) are up to six times more likely to develop hip osteoarthritis (OA) in either or both the intact and residual limb, which is primarily attributed to habitually altered joint loading due to compensatory movement patterns. However, joint loading patterns differ between limbs, which confounds the understanding of loading-induced OA etiology across limbs. It remains unknown if altered loading due to amputation results in bony shape changes at the hip, which is a known etiological factor in the development of hip OA. Retrospective computed tomography images were collected of the residual limb for 31 patients with unilateral TFA (13F/18M;​ age:​ 51.7 ± 9.9 y/o;​ time since amputation:​ 13.7 ± 12.4 years) and proximal femur for a control group of 29 patients (13F/16M;​ age:​ 42.0 ± 12.27 years) and used to create 3D geometries of the proximal femur. Femoral 3D geometric variation was quantified using statistical shape modeling (SSM), a computational tool which placed 2048 corresponding particles on each geometry. Independent modes of variation were created using principal component analysis. 2D radiographic measures of the proximal femur, including common measures such as α-angle, head neck offset, and neck shaft angle, were quantified on digitally reconstructed radiographs (DRRs). SSM results were then compared to 2D measures using Pearson correlation coefficients (r). Two-sample t-tests were used to determine if there were significant differences between the TFA and control group means of 2D radiographic measurements (p < 0.05). Patients with TFA had greater femoral head asphericity within the SSM, which was moderately correlated to head-neck offset (r = −0.54) and α-angle (r = 0.63), as well as greater trochanteric torsion, which was strongly correlated to the novel radiographic measure of trochanteric torsion (r = −0.78), compared to controls. For 2D measures, the neck-shaft angle was smaller in the TFA group compared to the control group (p = 0.01) while greater trochanter height was larger in the TFA group compared to the control group (p = 0.04). These results indicate altered loading from transfemoral prosthesis use changes proximal femur bony morphology, including femoral head asphericity and greater trochanter changes. Greater trochanter morphologic changes, though not a known factor to OA, affect moment arm and line of action of the primary hip abductors, the major muscles which contribute to joint loading and hip stability. Thus, chronic altered loading of the amputated limb hip, whether under- or overloading, results in bony changes to the proximal femur which may contribute to the etiological progression and development of OA.