BACKGROUND Several studies have assessed the association between hepatitis B virus (HBV) and hepatitis C virus (HCV) and non-Hodgkin's lymphoma. However, few studies are cohort by design, conducted within the Asian context and even fewer studies consider other lymphoid malignancies. The aim of this study was to assess the association between HBV and HCV and the risk of lymphoid malignancies among Japanese adults. METHODS The Japan Public Health Center prospective-based Study Cohort II was initiated in 1993/1994. 20,360 subjects with available data on HBV and HCV infection status from blood samples were followed up until the end of 2010 for an average of 16 years. During 324,139 person-years, 120 newly diagnosed cases of lymphoid malignancies were identified. Cox proportional hazards models were employed to calculate hazard ratios (HRs) and 95% confidence intervals (95%CIs). RESULTS Of 20,360 subjects, 508 were HBsAg positive, 11,035 were anti-HBc positive, and 1,129 subjects were anti-HCV positive at baseline. The presence of HBsAg was positively associated with malignant lymphoma, especially with non-Hodgkin's lymphoma (HR=3.56, 95%CI=1.37-9.18) and diffuse large B-cell lymphoma (HR=7.22, 95%CI=2.34-22.29). In contrast, no clear association was observed between the presence of anti-HBc and anti-HCV. CONCLUSIONS In conclusion, HBsAg but not anti-HBc or anti-HCV was positively associated with malignant lymphoma, particularly non-Hodgkin's lymphoma and diffuse large B-cell lymphoma in Japanese adults.