We investigated the detailed distribution of high-density lipoproteins (HDL) particle size in patients with cholesteryl ester transfer protein (CETP) deficiency. Serum samples pre-stained with Sudan black B were electrophoresed using 4-30% polyacrylamide gradient gels, and the Stokes diameter of HDL particles was determined in 23 patients with genetic CETP deficiency, nine patients with hyperalphalipoproteinemia and seven subjects with normal HDL cholesterol concentrations. The mean Stokes diameter of HDL particles in CETP deficient patients (11.2+/-0.6 nm) was significantly greater than hyperalphalipoproteinemia (10.7+/-0.3 nm, P<0.05) and normal subjects (9.5+/-0.4 nm, P<0.01). A significant relationship was found between mean HDL size and serum CETP mass concentrations (P<0.05). When the particle size of all detected HDL bands was investigated, extra-large HDL particles larger than 12 nm were found in 14 of the 23 patients with CETP deficiency, which were not found in any of the hyperalphalipoproteinemia patients or normal subjects. Serum low-density lipoproteins (LDL) cholesterol and total cholesterol concentrations were lower in CETP deficiencies with extra-large HDL particles than those in non-carriers (P<0.01). These results indicate that extra-large HDL may be an index to clarify the relationship between genetic CETP deficiency and atherosclerosis.