This study in 2006 estimated the hepatitis B virus (HBV) vaccination coverage in the Islamic Republic of Iran at the national and district levels in urban, rural and remote populations of 41 university health service areas. Of 21 905 children recruited to the study, vaccination coverage based on vaccination card records was 100% in 14, 15 and 10 of the 41 university areas for the 1st, 2nd and 3rd doses of HBV respectively. National levels of HBV1, HBV2 and HBV3 coverage were 98.9%, 98.8% and 98.4% respectively. The lowest HBV vaccination coverage rate was 90.7% (in a remote district). HBV vaccination coverage was at an acceptable level in Iranian children.