Background: Data about the association between hepatitis virus infection and colorectal neoplasia (CRN) are extremely limited. We examined the association between hepatitis B virus (HBV) and hepatitis C virus (HCV) infection with the risk of CRN. Methods: A cross-sectional study was performed on asymptomatic examinees who underwent a colonoscopy and serologic testing for hepatitis B surface antigen (HBsAg) and hepatitis C antibody (HCV Ab) between 2004 and 2015. Results: Of 155,674 participants who underwent serologic testing for HBsAg, 5476 (3.5%) were positive for HBsAg. The mean age of the study participants was 41.1 ± 9.1 years. The prevalence of CRN was higher in the HBsAg (+) than in HBsAg (-) participants (16.9% vs. 15.6%, p = 0.009). Even after adjusting for confounders, HBsAg positivity was correlated with an increased risk of CRN (odds ratio (OR), 1.10; 95% confidence interval (CI), 1.01-1.19; p = 0.025). Of 155,180 participants who underwent serologic testing for HCV Ab, only 240 (0.15%) were positive for HCV Ab. The prevalence of CRN was higher in HCV Ab (+) than in HCV Ab (-) participants (22.9% vs. 15.6%, p = 0.002). However, the association disappeared after adjusting for confounders (OR, 1.04; 95% CI, 0.72-1.50; p = 0.839). Conclusions: HBV infection was independently correlated with an increased risk of CRN.Our results indicate the possibility that HBV infection may contribute to colorectal carcinogenesis. Screening colonoscopy may have to be recommended more thoroughly for HBV-infected patients.