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In view of the possible involvement of apolipoprotein A2 (apoA2) in lipoprotein metabolism, we investigated the association between genetic variation of the APOA2 gene and lipid levels in Korean subjects with hypertriglyceridemia. The Mspl rare allele (M—) frequency in hypertriglyceridemic subjects was higher than that in normal control subjects, although the difference was not statistically significant. The M — allele frequency in a healthy population was higher in Koreans (0.27) than in Caucasian groups (0.10-0.21) studied previously. APOA2 polymorphism had an effect on plasma triglyceride levels in hypertriglyceridemic samples (p < 0.005). Triglyceride levels showed a gene dosage effect with the heterozygous genotype having an intermediate level between the two homozygous genotypes. However, the normal control group showed a lack of association with lipid traits. Thus the results suggest that, at least in Koreans, among hypertriglyceridemic subjects there is an association between APOA2 Mspl genotypes and triglyceride levels.