Objective  To study the distribution of hypoxia inducible factor（HIF）3A gene single nucleotide polymorphisms (SNPs) in Guangxi Han population and compare their distribution differences with different populations.    Methods  We conducted SNPscan technique to detect the genotypes of rs11672731 and rs2072491 on 286 Guangxi Han population included in the study and statistically analyzed the genotype and allele frequency and the HapMap-CEU, HapMap-HCB, HapMap-JPT, HapMap-GIH and HapMap-MEX data differences.    Results Three genotypes, AA, AG and GG, were found in rs11672731 of HIF3A,with frequency of 42.7%, 45.5% and 11.8%, respectively, the allele frequencies of A and G were 65.5% and 34.5%, respectively. Three genotypes of CC, CT and TT, were found for rs2072491 with frequency distributions of 47.6%, 43.0% and 9.4%, respectively, the allele frequencies of C and T were 69.1% and 30.9%, respectively. There was no significant differences in genotype and allele frequencies of rs11672731 and rs2072491 between different genders in Guangxi Han population (P>0.05). However, compared with the typing data of CEU, HCB, JPT, GHI, TSI and MEX from human genome project (HapMap), the genotype and allele frequencies of rs11672731 and rs2072491 were not significantly different from those of HCB and JPT (P>0.05). The genotype and allele frequencies of rs11672731 and rs2072491 were statistically different with the date of CEU, GIH, TSI and MEX published by the HapMap (P<0.05).    Conclusion  The polymorphisms of HIF3A gene rs11672731 and rs2072491 have differences on different populations.