Gallbladder (GB) stones have been associated with several metabolic factors and liver diseases. This community-based study aimed at investigating the prevalence rate of GB stones and its associated factors in a hepatitis B virus (HBV)/hepatitis C virus (HCV)-endemic township in southern Taiwan. A total of 1701 residents (689 males and 1012 females; mean age: 51.2 ± 16.0 years) were enrolled in this prospectively designed screening project. Serum biochemistry tests, including testing for levels of serum aspartate aminotransferase, alanine aminotransferase (ALT), hepatitis B surface antigen (HBsAg), and antibody to HCV (anti-HCV) were conducted. In addition, a hepatobiliary ultrasonographic (US) examination was also conducted. Of the 1701 residents, 243 (14.3%) and 475 (27.9%) were found to be positive for HBsAg and anti-HCV, respectively. Results of the US examination revealed the prevalence rate of GB stone and fatty liver to be 6.8% and 55.6%, respectively. Using univariate analyses we found that significantly higher proportions of the participants with GB stone were male, over 50 years of age, positive for anti-HCV (p = 0.001, p < 0.001, and p = 0.001, respectively), with significantly higher mean age and ALT level (p ≤ 0.001 and p = 0.048, respectively) than did those without GB stone. By applying multivariate analyses, male gender, positive anti-HCV, and older age (>50 year) were identified as independent factors associated with the formation of GB stones. Anti-HCV was associated with GB stones in males but not in females in both univariate and multivariate analyses. GB stones were found to have a prevalence rate of 6.8% in this HCV/HBV hyperendemic township and are associated with higher mean age. A correlation between chronic hepatitis C and GB stones is observed only among males.