Aim To investigate the frequency of variant at MspI Sites of apoA_Ⅰ gene and its relation to endogenous hypertriglyceridemia (HTG) in Chinese population. Methods The restriction fragment length polymorphisms (RFLPS) at two MspI sites in the 5'end at -78 bp and +83 bp of apolipoprotein A_Ⅰ gene were studied using PCR in 134 endogenous hypertriglyceridemics and 255 healthy subjects from a population of Chinese Han nationality in Chengdu area. The loci included MspI 1 (promoter region, -78 bp) and MspI 2 (intron 1,+83 bp)sites. Results Both in HTG group and control group, G/G genotype were the most frequent one, the frequencies of rare A alleles at -78 bp of apoA_Ⅰ gene in Chengdu were significantly higher than those in American and European Caucasians (0.300 vs 0.120～0.191,P<0.01), and the frequency of rare A allele in HTG group was significantly higher than that in the control group (0.350 vs 0.273,P<0.05). But no differences were found in the frequency of rare T allele for +83 bp. Both in the HTG group and control group, subjects with A/A had a higher serum mean concentration of TG, apoCⅢ and higher serum TG/HDLC ratio compared with the subjects with the genotypes G/A and G/G (P<0.05), and the serum apoCⅡ had a tendency to increase (P>0.05). Conclusions These results suggest that only the MspI 1 RFLP at -78 bp of apoA_Ⅰ gene is associated with endogenous hypertriglyceridemia to some extent in Chinese popuplation.