BACKGROUND: A universal newborn hepatitis B (HBV) vaccination program was introduced in the Northern Territory of Australia in 1990, followed by a school-based catch-up program. We evaluated the prevalence of hepatitis B infection in birthing women up to 20 years after vaccination and compared this to women born before the programs commenced. METHODS: A cohort of birthing mothers was defined from Northern Territory public hospital birth records between 2005 and 2010 and linked to laboratory confirmed notifications of chronic HBV, based principally on a record of hepatitis B surface antigen detection. Prevalence of HBV was compared between women born before or after implementation of the newborn and catch-up vaccination programs. FINDINGS: Among 10797 birthing mothers, 138 (1.3%) linked to a chronic HBV record. HBV prevalence was substantially higher in Aboriginal women compared to non-Indigenous women (2.4% versus 0.04%; p<0.001). Among 5678 Aboriginal women, those eligible for catch-up and newborn HBV vaccination programs had a significantly lower HBV prevalence than older women born prior to the programs: HBV prevalence respectively 2.2% versus 3.5%, (OR 0.61, 95%CI 0.43-0.88) and 0.8% versus 3.5% (OR 0.21, 95%CI 0.11-0.43). This represents a risk reduction of respectively 40% and 80% compared to unvaccinated women. INTERPRETATION: The progressively greater reduction in the prevalence of chronic HBV in adult Aboriginal women co-inciding with eligibility for catch-up and newborn vaccination programs is consistent with a significant impact from both programs. The use of data derived from antenatal screening to track ongoing vaccine impact is applicable to a range of settings globally. Copyright © 2012 Elsevier Ltd. All rights reserved.