Vitamin D exhibits immunomodulatory and antiproliferative effects through vitamin D receptor (VDR) in chronic infections and cancers. We genotyped the BsmI (rs1544410), ApaI (rs7975232) and TaqI (rs731236) polymorphisms of VDR gene in 250 Taiwanese chronic hepatitis B virus (HBV) carriers who were categorized into six phenotypes. After adjustment for age and sex, the frequencies of the VDR B/b, B/a, B/T, B/a/T in patients with hepatitis flare(s) were lower than those without (7 vs 20%, P ¼ 0.009; 1 vs 9%, P ¼ 0.004; 3 vs 10%, P ¼ 0.007; 1 vs 9%, P ¼ 0.005, respectively); in contrast, T/t, A/T, A/t, b/A/t were higher in flare(s) (8 vs 3%, P ¼ 0.003; 49 vs 34%, P ¼ 0.027; 2 vs 1%, P ¼ 0.004; 0.5 vs 0%, P ¼ 0.001, respectively).