Aim To investigate the relativity of apolipoprotein A5 gene (ApoA5) c.553G/T polymorphism in exon 4 with hyper total cholesterolemia (HTC) in Zunyi Han Nationality. Methods c.553G/T polymorphism of 101 HTC patients and 118 healthy individuals were tested by polymerase chain reaction and restriction fragment length (PCR-RFLP) assay. Results The genotype frequency of ApoA5 gene c.553G/T showed statistically difference between patients group and normal groups (P<0.05), and the distribution of ApoA5 c.553T gene in HTC group was significantly higher than normal group (P<0.05), therefore it had independent effect on HTC (OR=4.5,5%CI:1.269～17.296,P=0.020). It has more optical clinical significance comparing different blood lipid index ratio than one blood lipid index. Conclusion There was relativity between ApoA5 gene c.553G/T polymorphism and HTC in Zunyi Han Nationality. The c.553T gene was an independent risk factor for HTC.