We experienced a case of primary intestinal follicular lymphoma and premature atherosclerosis in a diabetic patient with familial partial lipodystrophy (FPL) that was detected when the patient was evaluated for laparoscopic sleeve gastrectomy (LSG). As FPL is generally considered to be rare, FPL is often underdiagnosed, especially in obese patients. Therefore, the prevalence of FPL is higher than previous estimates. Our case illustrates that clinicians should perform screening for atherosclerosis and malignancy at the preoperative evaluation and may need to perform metabolic surgery earlier to prevent the development of excess truncal fat, complicated diabetes and atherosclerosis in patients with FPL.