BACKGROUND The 2010 targets of the China Hepatitis B Prevention Programme were a prevalence of hepatitis B surface antigen (HBsAg) less than 1.0% for children less than five years old and less than 6.0% for the total population. This survey assessed the prevalence of Hepatitis B infection in Lianyungang, Jiangsu province, China in 2009-2010. METHODS Multistage sampling was used with 2372 subjects among 17 selected villages. Blood specimen collection and testing by enzyme-linked immunosorbnet assay (ELISA) were completed using the following markers for hepatitis infection: HBsAg and antibody to HBsAg (anti-HBs); hepatitis B e antigen (HBeAg) and antibody to HBeAg (anti-HBe); and hepatitis B core antibody (total anti-HBc). The data were analysed with Epi Info, version 3.3.2. RESULTS The prevalence of HBsAg was 2.4% (95% Confidence Interval [CI]: 1.8-3.0; Adjusted Prevalence [AP] 2.9%); anti-HBs prevalence was 51.1% (95% CI: 49.1-53.1; AP 49.2%) and total anti-HBc prevalence was 41.7% (95% CI: 39.8-43.7; AP 45.5%). The prevalence of HBsAg and total anti-HBc positivity increased from young to older age groups, yet the prevalence of anti-HBs positivity decreased from young to older age groups (P < 0.001 for all). There was no difference in the prevalences of HBsAg and anti-HBs among females and males (P = 0.108 and 0.089), but females had a higher prevalence than males for total anti-HBc positivity (P < 0.001). CONCLUSIONS This survey showed that in 2010 the prevalence of HBsAg among children aged less than five years was lower than the national target of 1.0% and that the prevalence of HBsAg for the total population was lower than the national target of 6.0%.