Malformations of the lower limbs are rare and heterogeneous anomalies. Some congenital anomalies involving face, gastrointestinal system, skeletal system, urogenital system, heart, lung and diaphragma associated with lower limb malformations have been described in the literature. Here, we report a case of left proximal femoral focal deficiency (PFFD) together with fibular aplasia associated with left undescended testis and hypospadias. The putative embryologic mechanisms of lower limb defects and their possible association with lower urogenital tract malformations are also discussed.