The exon 16 of the cholesteryl ester transfer protein (CETP) gene was screened for possible mutations in patients with low plasma high-density lipoprotein cholesterol (HDL-C) levels and established coronary heart disease. 115 men who had undergone coronary bypass surgery were compared with a random population sample of 515 subjects. A single G to A substitution at base pair 1696 was found in the 3' untranslated region of the CETP gene. Among the patients with low HDL-C, the plasma CETP activity was 29% lower (P = 0.002) in the subjects homozygous for the mutation than in those with other genotypes. The same effect was observed in the random population sample (P = 0.02). The mutation did not affect the plasma lipid or lipoprotein values, although the mean HDL-C tended to be slightly higher and the ratio of cholesterol content in the apo B-containing lipoproteins to HDL-C slightly lower in the homozygotes compared with the other genotypes. In conclusion, we describe a prevalent mutation at the CETP gene locus associated with low plasma CETP activity. Our results support previous findings suggesting that the genes in chromosome 16 may be important in the regulation of reverse cholesterol transport and in protection against coronary heart disease.