Occult hepatitis B virus (HBV) infection (OBI) is hepatitis B surface antigen (HBsAg) negative but with detectable HBV DNA. Although HIV infection has been reported to be a risk factor for OBI, the prevalence and clinical features of OBI in Japanese HIV infected patients have not been documented. This retrospective, single-center study was conducted to determine the prevalence and characteristic of OBI in Japanese antiretroviral therapy (ART) naïve HIV infected patients. OBI was defined as the presence of serum HBV DNA but without detectable HBsAg. Of the 147 ART naïve HIV infected patients, OBI was detected in 9 (6.1%) patients; 2 (4.3%) of 47 with both anti-HBs and anti-HBc positive, 6 (27.3%) of 22 with anti-HBc alone, and 1 (2.0%) of 50 with both anti-HBs and anti-HBc negative. The mean HBV DNA level was low at 28.7 ± 18.2 IU/mL. The proportion of OBI patients with anti-HBc alone was significantly higher than that of non-OBI patients (66.7% vs 14.5%, P = 0.001). In addition, the prevalence of AIDS (acquired immunodeficiency syndrome)-defining illnesses in the OBI group was significantly higher than in the non-OBI group (77.8% vs 35.5%, P = 0.001). No significant difference was found in the CD4 count or alanine aminotransferase levels of these two groups. This is the first study to reveal the prevalence and clinical features of OBI in Japanese HIV-infected patients. The persistence of anti-HBc alone and AIDS-defining illnesses were associated with the occurrence of OBI in these patients.