A cross-sectional study was carried out in employees of 17 Greek companies with the aim of assessing the prevalence of hepatitis B (HBV) and hepatitis C (HCV) virus, identifying associated prognostic/risk factors and evaluating the effectiveness of a questionnaire as a pre-screening tool. All participants were asked to complete a questionnaire and a random sample of them was asked to provide a blood sample for hepatitis B core antibody (anti-HBc), hepatitis B surface antigen (HBsAg) and antibodies to hepatitis C (anti-HCV) testing. Individual questions or combinations of them were evaluated in terms of their ability to detect HBV or HCV(+) cases. Of 9085 eligible employees, 6074 (67%) completed the questionnaire. Of 990 samples obtained, 19.9% were anti-HBc(+), 2.6% HBsAg(+) and 0.5% anti-HCV(+). All anti-HCV(+) cases had multiple parenteral risk factors. Multiple logistic regression identified associations between anti-HBc and older age, family members with chronic hepatitis, job category and history of transfusion before 1992. HBsAg(+) was associated with older age and history of transfusion before 1992. None of the risk/prognostic factors had sufficient sensitivity and specificity for HBV but report of at least one risk factor identified all HCV(+) cases. Anti-HCV screening of those with at least two parenteral risk factors not only identified all anti-HCV(+) cases but also resulted in 86% decrease in the screening cost. Under the light of recent treatment advances, targeted questionnaire-based screening of asymptomatic people may prove to be a cost-effective way to face hepatitis C.