In regions that are hyperendemic for chronic hepatitis B virus (HBV) infection, prevalence of and risk factors associated with isolated anti-hepatitis B core antibody (anti-HBc) in HIV-positive patients are less well described. HIV-positive patients who were tested for hepatitis B surface antigen (HBsAg), anti-hepatitis B surface antibody (anti-HBs) and anti-HBc at designated hospitals for HIV care in Taiwan were included for analysis. HBV DNA was detected by real-time polymerase chain reaction in patients with and without isolated anti-HBc. Of 2351 HIV-positive patients, 450 (19.1%) were HBsAg positive, 411 (17.5%) were anti-HBc positive alone and 963 (41.0%) for both anti-HBs and anti-HBc. Compared with patients who were positive for both anti-HBs and anti-HBc, patients with isolated anti-HBc were older, less likely to have anti-hepatitis C virus antibody (anti-HCV), had lower CD4 lymphocyte counts and higher plasma HIV RNA loads. Older age (adjusted odds ratio, 1.029; 95% confidence interval, 1.015-1.043) and CD4 <100 cells/microL (adjusted odds ratio, 1.524; 95% confidence interval, 1.025-2.265) were independently associated with isolated anti-HBc by logistic regression, while presence of anti-HCV and injecting drug use were not. HBV DNA was detectable in 8.3% of 277 patients with isolated anti-HBc and 14.3% of 56 patients with both anti-HBs and anti-HBc (P = 0.160). In a country hyperendemic for HBV infection, HIV-positive patients at older age and with CD4 <100 cells/microL were more likely to have isolated anti-HBc, suggesting that compromised immunity plays a role in the presence of this marker.