We herein report a case of premature atherosclerosis in a patient with familial partial lipodystrophy (FPL), diabetes mellitus, hypertension and hypertriglyceridemia. Sequencing of the candidate genes LMNA, PPARG and CAV1 associated with FPL revealed no genetic abnormalities, which indicated the activity of a novel gene in this patient. The patient's son showed milder fat loss and similar fat distribution compared to the proband; however, the son showed no signs of any atherosclerotic disease. Although a cluster of atherogenic risk factors is likely to be the primary causes of atherosclerosis in our patient, other factors, including an unknown gene associated with FPL, the severity of fat loss and gender, might affect the development of atherosclerosis.