To elucidate the importance of aflatoxin in the etiology of hepatocellular carcinoma (HCC), a community-based cohort study combined with molecular dosimetry of aflatoxin exposure was performed in the Penghu Islets where the HCC mortality rate is highest in Taiwan. A total of 6,487 residents aged 30 to 65 years were recruited in the two-stage screening survey and underwent regular follow-up examination. Among 33 newly diagnosed HCC cases, 31 (94%) were chronic hepatitis B surface antigen (HBsAg) carriers and 3 (9%) were positive for antibodies against hepatitis C virus (HCV). Among 20 HCC patients and 86 matched healthy controls whose serum samples were tested for aflatoxin B1 (AFB1)-albumin adducts by competitive enzyme-linked immunosorbant assay (ELISA), 13 (65%) HCC patients and 32 (37%) matched controls were seropositive, showing a statistically significant multivariate-adjusted odds ratio of 5.5 with a 95% confidence interval of 1.2 to 24.5. The results imply the elevated risk of HCC among Penghu residents may be attributable to their heavy exposure to aflatoxins and high HBsAg carrier rate.