1. A genetic polymorphism of apolipoprotein (apo) C-III was studied in 49 Caucasian patients with extra-coronary atherosclerosis demonstrated by angiography. 2. Twelve patients (24%) possessed an uncommon allelic variant of the apo A-I/C-III gene cluster compared with two (4%) in 50 healthy controls ( P < 0.01). 3. Of 27 patients with carotid atherosclerosis, 22% had the uncommon genotype ( P < 0.02), and in aortofemoral atherosclerosis ( n = 22) 27% possessed the uncommon variant ( P < 0.01). 4. When normotriglyceridaemic subgroups ( n = 32) with arterial disease were studied the difference in genotype frequencies persisted, 22% having the uncommon allele ( P < 0.01), suggesting that such genetic variants have effects independent of circulating levels of plasma lipids.