Objective To explore the relationship between metabolic syndrome and ApoA5 gene polymorphism and serum concentration. Methods 100 patients with metabolic syndrome(MS group) and 100 healthy people(control group) were enrolled in this study. The ApoA5 serum concentration of two groups were measured by using enzyme-linked immunosorbent assay(ELISA), the genotypes of ApoA5-1131T＞C polymorphism were analyzed by polymerase chain reaction-restriction fragment length polymorphism, and fasting blood glucose (FBG), total cholesterol (TC), triglyceride (TG), low density lipoprotein (LDL), high density lipoprotein (HDL) and white blood cell, hemoglobin,platelet, liver and kidney function were measured. Results MS group was compared with control group. In MS group, the ApoA5 serum concentration was significantly lower[(96.68±18.09)ng/ml vs (128.32±23.78)ng/ml,P＜0.01], while the triglycerides levels were obviously higher[(2.35±1.07)mmol/L vs (1.62±1.13)mmol/L,P＜0.01], and ApoA5-1131C allele frequency was higher than that in control group (30% vs 16.5%,P＜0.05). Conclusions The ApoA5 serum concentration in metabolic syndrome was decreased, and ApoA5-1131C was associated with metabolic syndrome.