To explore the relationship between HBV infection and the genotypes and allele frequencies of CIITA G-944C gene polymorphism in three minority populations (Jinuo, Dai and Aini population) in Xishuangbanna district, Yunnan province. Polymerase chain reaction and sequencing method were used to study the genotypes and allele frequencies distributions of CIITA G-944C gene polymorphism in those three populations. Relationship between the genotypes distribution and HBV infection results were also analyzed. The rates on HBV infection and HBsAg carrier status in Aini minority population were 89.2% and 16.3%, which were significantly higher than in Jinuo (27.9% and 3.9%, χ(2) = 135.196 and 10.361, P = 0.000 and 0.001) and Dai population (44.9% and 6.6%, χ(2) = 96.783 and 8.748, P = 0.000 and 0.003) while among Aini population it was significantly different with the other two minority populations. The CC genotype and C allele frequencies were more distributed in Aini population than in the other two minority populations. In contrast, the GG genotype and G allele frequencies were lower than the other two minority populations, with χ(2) rates between Aini and Jinuo population were 11.841 and 12.208 and the P as 0.003 and 0.000 respectively while the χ(2) rates between Aini and Dai population were 23.902 and 20.220 with P value as 0.000 and 0.000. The genotypes frequencies of CIITA G-944C was significantly different in the infected individuals (IF) group and health control (HC) group in Jinuo population (χ(2) = 6.150 and 4.911, P = 0.046 and 0.027). When compared with HBsAg(+) group and HBsAg(-) group, the genotypes and allele frequencies were different in Aini population and the total three minority populations (χ(2) rates in Jinuo minority were 8.650 and 5.034 with P values as 0.013 and 0.025). However, the χ(2) rates in the whole population were 13.047 and 9.416 with P values as 0.001 and 0.002, respectively. The distribution of CC genotype and C allele gene in HBsAg(+) group was increasing. Data from non-condition logistic regression analysis and adjusting for confounding factors, the HBsAg(+) group had a significantly increase of HBsAg(-) group under the C allele Recessive Model (P = 0.000; OR = 2.964; 95%CI: 1.609 - 5.460). The genotypes and allele frequencies distribution of CIITA G-944C were different in the three ethnic populations. Polymorphism of this gene was closely associated with HBsAg carrier. The CC genotype patients were more easily to become HBsAg carrier.