Cholesteryl ester transfer protein (CETP) is understood to play a regulatory role in HDL cholesterol (HDLC) metabolism. In this study, the effect of CETP genotypes on plasma lipid and lipoprotein levels in 348 Vietnamese girls (aged 7-9) with different nutritional conditions was analyzed. The two mutations, intron 14 G(+1)-to-A (I14A) and Asp 442 to Gly within exon 15 (D442G), and the TaqIB polymorphism in the CETP gene were identified by an Invader assay. The D442G mutation was present with a frequency of 0.034, while the I14A mutation was absent. HDLC levels were significantly higher in carriers of the D442G mutation than in noncarriers, regardless of the nutritional status. Low-density lipoprotein (LDL) cholesterol and triglyceride levels were not significantly lower in carriers of D442G mutation. The frequency of the TaqIB2 allele was 0.34, which was lower than that observed in other Asian populations. TaqIB2B2 carriers also had significantly higher HDLC levels, but this association was weaker than that of the D442G mutation. Overall, genetic variations at the CETP gene locus may account for a significant proportion of HDLC variation in Vietnamese children.