To determine whether Taq I T/C and Fok I C/T polymorphisms of vitamin D Receptor (VDR) gene was associated with the outcomes of hepatitis B virus (HBV) infection. A total of 212 HBV self-limited infection individuals, 244 asymptomatic HBsAg carriers and 391 chronic hepatitis B (HB) patients were recruited to conduct a case-control study. VDR-Taq I T/C and VDR-Fok I C/T polymorphisms were examined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The frequency of VDR-Fok I allele C in the chronic HB patients was 45.8%, significantly higher than 38.2% of the self-limited infection individuals (chi(2) = 6.43, P = 0.01). The frequencies of VDR-Fok I genotypes TT, TC, and CC in HB patients were 30.7%, 47.1%, and 22.2% respectively, and 41.0% (TT), 41.5% (TC), and 17.5% (CC) in the self-limited infection individuals. There was a statistically significant difference between HB patients and self-limited infection individuals (chi(2) = 6.76, P = 0.03). The results of univariate analysis showed that the subjects carrying VDR-Fok I CC/TC genotype had 1.57-fold elevated risk for developing chronic HB when they were infected HBV (OR = 1.57, P = 0.01). A multiple logistic regression analysis revealed that VDR-Fok I CC/CT was independently associated with chronic HB after adjusting both potential confounding effects of gender (OR = 1.70, P = 0.021). The statistically significant association between TaqI T/C polymorphism and outcome of HBV infection was not demonstrated in the study. The frequency of haplotype TC of VDR-TaqI and Fok I in HB patients was 2.3080%, significantly higher than 0.5391% of the self-limited infection individuals (chi(2) = 6.08, P = 0.01). However, the frequency of haplotype TT in the HB patients was 1.5283%, significantly lower than 3.7061% of the self-limited infection individuals (chi(2) = 5.65, P = 0.02) and 3.4820% of the HBV carriers (chi(2) = 5.12, P = 0.02). VDR gene polymorphism is probably an influence factor on the genetic susceptibility of HBV infection.