Familial lecithin:cholesterol acyltransferase (LCAT) deficiency is a rare genetic disorder of the lipid metabolism caused by the absence of LCAT activity in plasma. It is not generally accompanied by atherosclerosis in spite of low high-density lipoprotein cholesterol levels nor by diabetes mellitus. However, reports of long-term follow-up or autopsy findings are rare, and the true incidence of atherosclerosis in LCAT deficiency is not clear. We report on the long-term observation of a patient with familial LCAT deficiency who developed renal failure, diabetes mellitus, and marked atherosclerosis. The patient died of sepsis from foot ulcers 7 years after starting hemodialysis and 13 years after the diagnosis. Marked atherosclerosis characterized by medial calcification in small arteries was observed at autopsy. The genesis of the atherosclerosis seemed to be on the basis of a combination of factors.