Aim To determine the allele frequencies of genetic variants 373 Ala→Pro and 451 Arg→Gln of cholesteryl ester transfer protein (CETP) and to explore their potential impacts on serum lipid metabolism. Methods The genotypes in CETP codon 373 and 451 in 91 German healthy students and 409 angiographically confirmed coronary heart disease (CHD) patients were respectively analyzed using the allele specific technique of mutagenically separated polymerase chain reaction (MS-PCR) and their serum lipid parameters were determined.Results It is demonstrated that genetic variants 373 Ala→Pro and 451 Arg→Gln are frequent mutations with allele frequencies around 3% to 5% presented in the healthy individuals as well as in the CHD patients. The high density lipoprotein cholesterol (HDLC) level was significantly decreased in the 373-Pro and 451-Gln alleles heterozygotic carriers in both examined cohorts compared with those in the wild type individuals. The increasing of serum triglyceride (TG) in the mutant alleles carriers was only observed in the healthy volunteers. It was also found that these two genetic variants do not always emerge in the linkage form. Conclusion It is suggested that these two mutations together would possess the phenotype of decreasing HDLC and increasing TG levels.