Background and Aims Hepatitis B virus (HBV) and Hepatitis C virus (HCV) infections are major worldwide public health problems. The objectives of this study were to evaluate the seroprevalence and epidemiological profile of hepatitis B and hepatitis C, to determine the impact of the national vaccination programme against hepatitis B on the prevalence of the hepatitis B surface antigen (HBsAg) carrier and the antibody to hepatitis B surface antigen (anti-HBs) occurrence rate among 0-14 year-old children in southeast Turkey. Methods The seroprevalence of hepatitis B and hepatitis C markers was evaluated retrospectively in a group of 10,391 children who were admitted to a tertiary hospital, the Diyarbakir Education and Research Hospital, from January 2005 to December 2008, in order to obtain a better understanding of the regional hepatitis seroprevalence. Children were divided into three different age groups: pre-education period (0-6 years), primary school period (7-12 years) and secondary school period (13-14 years). Samples were analyzed for HBsAg, hepatitis B e antigen (HBeAg), antibody to HBeAg (anti-HBe), anti-HBs positive/antibodies to hepatitis B core antigen (anti-HBc) positive, isolated anti-HBs and antibodies to Hepatitis C virus (anti-HCV) using a commercially available enzyme-linked immunosorbent assay (ELISA). Results The mean age of all participants was 8.5± 2 years (range, 0-14). The overall percentages for the prevalence of HBsAg, HBeAg, anti-HBe and anti-HCV were 8.1%, 2.1%, 5.9% and 0.5%, respectively. HBsAg seroprevalence differed significantly by age and gender (P < 0.001). HBeAg seroprevalence was high in the earliest years (P < 0.01). The overall prevalence of anti-HCV did not differ significantly by age (P > 0.5) but differed by gender (P < 0.001). The overall percentages for the prevalence of isolated anti-HBs and anti-HBs positive/anti-HBc positive were 34.2% and 56.9%,respectively. Conclusions Our study sheds new light on hepatitis seroprevalence in southeastern Turkey. For example, 1) The seroprevalence of hepatitis B in southeast Turkey is still at its highest rate, according to the averages reported in other studies conducted in the same and different regions of Turkey; and it has not decreased, as reported previously. 2) HBeAg seroprevalence in the earliest years of childhood is high in our study; this is evidence for early acquisition of the infection.3) Isolated anti-HBs positive and anti-HBs positive/anti-HBc positive prevalence is high; given these features, it is obvious that despite the high incidence of vaccinated children, the prevalence of hepatitis B is increasing; and children acquire these viruses in their earliest years. 4) We found the overall prevalence of HCV infection unchanged. Our region has a low endemicity for HCV.