Congenital generalized lipodystrophy (CGL), or Berardinelli–Seip syndrome (BSCL), is a part of lipodystrophic syndromes that constitute a heterogeneous group of genetic or acquired generalized or partial body fat loss disorders. It is a rare autosomal recessive disease characterized by a near-absence of adipose tissue from birth or early infancy and severe insulin resistance. CGL is classified as type 1–4, depending on the gene involved, and bone lytic lesion is found frequently in type 1 especially in long bones, but reported to be rare in type 2. Here we report an active lifestyle 25-year-old woman with type 2 CGL showing multiple bone lytic and pseudo-osteopoikilosis lesions in hands and feet. Radiograph bone survey showed no apparent abnormality in pelvic bone or axial skeletons. Bone marrow was completely absent and extra-skeletal general fat loss was also evident in whole-body magnetic resonance imaging sparing the orbital, axial, sole, and palmar regions. Radiographic bone survey is important even for type 2 CGL to find the change of bones to provide direction of preventing excessive overload or activity.