Aim To investigate the relationship between apolipoprotein A5 gene-1131T>C polymorphism,S19W polymorphism and the serum lipid levels in Chinese patients with endogenous hypertriglyceridemia. Methods The restriction fragment length polymorphism(RFLP) of-1131T>C and S19W was studied using polymerase chain reaction(PCR) in 200 healthy subjects and 182 subjects with endogenous hypertriglyceridemia from a population of Chinese Han nationality in Jiangsu Province. Results The frequencies of T,C alleles of-1131T>C polymorphism were 52.7%,47.3% and 67.0%,33.0% in HTG group and control group,respectively. There were significant differences in allele frequencies between HTG group and control group(p<0.05). The relationship between S19W polymorphism and the disease risk was not found. Conclusion C allele of apolipoprotein A5-1131T>C polymorphism is associated with higher serum TG.