Objective The aim of this study was to evaluate whether PRDM16 gene polymorphisms were associated with dyslipidemia. Methods The polymorphisms of rs2651899, rs2236518, rs870171, and rs2282198 in PRDM16 gene in 528 participants were genotyped by the method of snapshot or ligase detection reaction. The genotype differences and the allele differences between the case group and the control group were analyzed. Linkage disequilibrium analysis was performed with SHE-sis online software. The interaction between rs2651899, rs2236518, rs870171, rs2282198 and gender, age, BMI were analyzed by MDR software. Results The frequency of allele A in rs2651899 locus was significantly higher in low HDL-C group compared with that in control group[OR(95%CI)=1.32(1.02-1.71), P=0.033]. The frequency of A/C genotype in rs870171 was significantly different between LDL-C abnormal group and control group[OR(95% CI)=1.97(1.01-3.86), P=0.037]. There may be interaction between rs2236518 and sex, which is a risk factor for low HDL-C[Model Ⅱ: OR(95% CI)=1.958(1.366-2.809), P<0.01]. There may be interactions among rs2651899, rs2236518, rs870171, and rs2282198, which seemed to be risk factors for lower HDL-C[Model Ⅳ: OR(95% CI)=3.991(2.707-5.884), P<0.01]. rs870171, rs2282198 may have interaction with age, which is a risk factor for high LDL-C [Model Ⅶ: OR(95%CI)=3.991(2.707-5.884), P<0.01]. Conclusion Allele A of rs2651899 may be a risk factor to low HDL-C. Under the codominant inheritance patterns, genotype A/C of rs870171 may be a risk factor to high LDL-C. In addition, there may be interaction between SNPs with gender and age.