The early detection and prompt treatment of hepatocellular carcinoma (HCC) may prolong life and improve the quality of life of affected patients. In order to compare sensitivity and specificity of various screening biomarkers, identify subjects with a high risk of developing HCC, and estimate prevalence and incidence of HCC among subjects, a community-based HCC screening program was implemented in Sanchi, Chutung, Potzu, and Kaohsu, Taiwan Island as well as Makung, Huhsi and Paihsa in Penghu Islets. First stage screening of HCC was based on serological markers including hepatitis B surface antigen (HBsAg), antibody against hepatitis C virus (anti-HCV), alpha-fetoprotein (AFP > or = 20 ng/mL), alanine transaminase (> or = 40 IU/L), and aspartate transaminase (> or = 45 IU/L); as well as history of liver cirrhosis or HCC among first-degree relatives. Subjects who were positive for at least one of above six first-stage criteria were referred for second-stage screening by abdominal ultrasonography. Confirmatory diagnosis of HCC was made in suspicious cases according to aspiration cytology surgical pathology, digital substracted angiogram and/or computed tomography. A total of 12,026 men in seven study townships and 1,800 women in two townships in Penghu were recruited for first-stage screening (response rate: men, 25.5%; women, 46.8%). The positive rates for first-stage screening were 30.9% men and 34.6% women. The response rates for second-stage screening were 91% men and 90.5% women. Age-standardized prevalence of HCC per 1,000 subjects was 5.2 for men and 0.8 for women in Penghu Islets and 1.2 for men on Taiwan island. Among five serological biomarkers, HBsAg carrier status had the highest sensitivity (88.2%) and AFP had the second highest sensitivity (43.1%). The specificity of these markers was highest for AFP (99.0%) and lowest for HBsAg carrier status (80.3%). There were 16 new HCC cases identified after an intensive follow-up of 137 cases affected with liver cirrhos is giving an annual HCC incidence rate of 5.3%, while the rate for non-cirrhotic subjects who were positive on first-stage screening was only 0.15%. The combination of HBsAg and AFP for the first-stage screening and abdominal ultrasonography for the second-state screening seems valid for the early detection of HCC, but its cost-effectiveness remains to be elucidated by a longer follow-up study.