Objective: The association between Sjögren's syndrome (SS) and chronic hepatitis virus infection is inconclusive. Hepatitis B (HBV) and hepatitis C virus (HCV) infections are highly prevalent in Taiwan. We used a population-based case-control study to evaluate the associations between SS and HBV and HCV infections. Materials and Methods: We identified 9,629 SS patients without other concomitant autoimmune diseases and 38,516 sex- and age-matched controls without SS from the Taiwan National Health Insurance claims data between 2000 and 2011. We utilized multivariate logistic regression to estimate the odds ratios (ORs) and 95% confidence intervals (CIs) of the associations between SS and HBV and HCV infections. Sex- and age-specific (<55 and ≥55 years) risks of SS were evaluated. Results: The risk of SS was higher in patients with HCV than in those without chronic viral hepatitis (OR = 2.49, 95% CI = 2.16-2.86). Conversely, HBV infection was not associated with SS (OR = 1.10, 95% CI = 0.98-1.24). Younger HCV patients were at a higher risk for SS (<55 years: OR = 3.37, 95% CI = 2.62-4.35; ≥55 years: OR = 2.20, 95% CI = 1.84-2.62). Men with HCV were at a greater risk for SS (women: OR = 2.26, 95% CI = 1.94-2.63; men: OR = 4.22, 95% CI = 2.90-6.16). Only men with chronic HBV exhibited a higher risk of SS (OR = 1.61, 95% CI = 1.21-2.14). Conclusion: HCV infection was associated with SS; however, HBV only associated with SS in men.