Our purpose was to compare HDL subpopulations, as determined by nondenaturing two-dimensional gel electrophoresis followed by immunoblotting for apolipoprotein A-I (apoA-I), apoA-II, apoA-IV, apoCs, and apoE in heterozygous, compound heterozygous, and homozygous subjects for cholesteryl ester transfer protein (CETP) deficiency and controls. Heterozygotes, compound heterozygotes, and homozygotes had CETP masses that were 30, 63, and more than 90% lower and HDL-cholesterol values that were 64, 168, and 203% higher than those in controls, respectively. Heterozygotes had ف 50% lower pre  -1 and more than 2-fold higher levels of ␣ -1 and pre ␣ -1 particles than controls. Three of the five heterozygotes' ␣ -1 particles also contained apoA-II, which was not seen in controls. Compound heterozygotes and homozygotes had very large particles not observed in controls and heterozygotes. These particles contained apoA-I, apoA-II, apoCs, and apoE. However, these subjects did not have decreased pre  -1 levels. Our data indicate that CETP deficiency results in the formation of very large HDL particles containing all of the major HDL apolipoproteins except for apoA-IV. We hypothesize that the HDL subpopulation profile of heterozygous CETP-deficient patients, especially those with high levels of ␣ -1 containing apoA-I but no apoA-II, represent an improved antiatherogenic state, although this might not be the case for compound heterozygotes and homozygotes with very large, undifferentiated HDL particles. -Asztalos, B. F., K. V. Horvath, K. Kajinami, C. Nartsupha, C. E. Cox, M. Batista, E. J. (1, 2). The major role of CETP is a net transfer of CE from HDL to TG-rich lipoprotein (TRL) and of LDL and TG from TRL to LDL and HDL. CETP mRNA is expressed in several tissues, but the majority of circulating CETP originates from the liver (3).CETP plays a key role in HDL metabolism (4). It regulates total plasma HDL-cholesterol (HDL-C) level and also facilitates the remodeling of HDL particles (5). A high CETP concentration correlates with a low HDL-C level, a strong risk factor for coronary artery disease (6). On the other hand, Asian subjects with CETP deficiency have markedly increased HDL-C (3-to 6-fold) and apoA-I concentrations (7-9). CETP deficiency-induced increase in HDL-C level is mainly found in the large HDL2 subclass. Moreover, the average HDL size of CETP-deficient subjects is significantly increased and enriched in cholesterol (10). These large HDL particles have been reported to be less effective in promoting cholesterol efflux from lipidloaded macrophages than HDL particles of control subjects (11).Several mutations of the CETP gene have been identified as causes of CETP deficiency and increased HDL-C levels. These include a G-to-A substitution within intron 14 at the donor splice site (Int14A), a mutation that is present in up to 2% of the total Japanese population and in as many as 27% of people in the Omagari area of Japan, as well as a missense mutation in exon 15 (D422G) present in up to 7% of the Japanese...