Congenital generalized lipodystrophy (CGL) is a rare genetic disease characterized by the absence of body fat from birth. Focal bone lesions have also been reported, but their pathophysiology is poorly understood. To characterize skeletal abnormalities further in 3 patients with CGL, we employed whole-body radiographic skeletal surveys, magnetic resonance imaging (MRI, including gadolinium enhancement), and triple phase technetium-99m methylene diphosphonate bone scintigraphy. Radiographs showed numerous focal lesions within the long bones, as described in other reports. MRI showed that the entire marrow space of the long bones was abnormal and was characterized, at least in part, by the absence of marrow fat. Prolonged T1 and T2 times and marked gadolinium enhancement were observed in radiographically normal-appearing long bone. Radiographically lytic lesions occasionally demonstrated fluid-fluid levels on MRI and enhanced peripherally after gadolinium infusion. Bone scintigraphy findings such as periarticular hyperemia were relative subtle. We conclude that the appendicular skeleton of patients with CGL is diffusely abnormal and is predisposed to focal osteolysis and cyst formation.