As a result of the several hip joint disorders seen on the hip joint components, shape deformities occur in the morphological structure of the proximal femurs and femoral heads. Quantification of the shape deformities in related hip joint components is a crucial task since it may provide assistive information to clinical experts and surgeons in clinical treatment, assessment and prognosis processes. In this article, a preliminary study handling the 3D shape deformity quantification of the abnormal proximal femurs is presented. The shape deformity of the abnormal proximal femurs in bilateral hip joint images are quantified directly by using the morphological structure of the contralateral healthy proximal femurs without a need for a statistical shape model. For this purpose, segmentation maps of the bilateral proximal femurs are registered in 3D by performing a rigid transform method, and the regions outside the intersection volume are quantified as the shape deformities. To evaluate the proposed study, a total of 13 bilateral hip magnetic resonance imaging (MRI) sequences of 13 patients with Legg-Calve-Perthes disease (LCPD) were used. The deformity ratios observed in experiments are quite promising and consistent with the Waldenstrom classification system stages of the LCPD. The shape deformity ratios of the pathological proximal femurs in 3D were quantified as 18.02% (±04.84), 26.41% (±07.54), 31.21% (±11.07), and 36.84% (±09.33), respectively for the Initial, Fragmentation, Reossification, and Remodelling stages of LCPD in this preliminary study.