Previous studies have shown that CETP and LIPC mutations contribute to hyperalphalipoproteinemia (HALP) in some populations. We investigated whether activities in cholesteryl ester transfer protein (CETP) and hepatic lipase (HL) contribute to HALP in the Thai population and performed genetic analyses of the CETP and LIPC genes. We recruited 38 individuals with high-density lipoprotein cholesterol (HDL-C) levels of at least 2.59 mmol/L (100 mg/dL) (HALP group) and an equal number of individuals with normal serum HDL-C levels (control group). The CETP and HL activities were determined in both groups. Genetic analyses covering all the coding regions and exon-intron junctions of the CETP and LIPC genes were performed in subjects who had low CETP activity and HL activity, respectively. The mean CETP and HL activities were significantly lower in the HALP group than in the control group (34 +/- 4 vs 44 +/- 3 pmol/[microL h], P = .04 and 150 +/- 17 vs 227 +/- 16 nmol free fatty acid/[mL min] P = .002, respectively). Of the 38 individuals with HALP, 19 and 16 were found to have low CETP activity and HL activity, respectively. Of the 19 subjects with low CETP activity, 6 subjects were found to be heterozygous for a known functionally relevant c.1325A>G (D442G) mutation. The other subject was found to be heterozygous for a novel deletion mutation, c.734_737delTCCC mutation. Of the 16 subjects with low HL activity, 8 and 2 subjects were found to be heterozygous for known variants, c.283 G>A (V73M) and c.1068A>C (L334F), respectively. These variants have previously been shown not to be associated with HALP. Another subject was found to be heterozygous for a novel missense mutation, c.421G>A (G119S). Its amino acid change, absence in controls, evolutionary conservation, occurrence in functionally important domain, and predicted damaging function suggested that the G119S mutation is functionally relevant. Two novel mutations in the CETP and LIPC genes found in this study are likely to be the causes of low enzyme activities and elevated HDL-C levels.