AIM: To evaluate the impact of reorganisation of the health service and a change in the definition used to collect immunisation coverage statistics on vaccine coverage data in England. METHODS: Denominator data from the Cover Of Vaccination Evaluated Rapidly (COVER) programme, the national programme for the collection of immunisation coverage statistics, were compared to the Office for National Statistics (ONS) population data; the impact of any discrepancies between the two data sources on vaccine coverage was assessed. RESULTS: ONS populations were generally larger than COVER populations. This was particularly true for 2002, the year Primary Care Trusts (PCTs) came into existence, suggesting that some children are being missed by the COVER programme. On average, in 1998-2001 around 10,000 children per year (approximately 2%) were lost to the COVER population estimates compared to data from ONS. This increased to around 20,000-40,000 (approximately 3-8%) children in 2002, but decreased again in 2003 to 2000-8000 (approximately 1%) children. Assuming all the "lost" COVER children were vaccinated, vaccine coverage appeared very similar to that seen in the COVER programme for all antigens. However, assuming all the "lost" children were unvaccinated, coverage would be substantially lower for all antigens (range 2.7-3.5%). DISCUSSION: This analysis provides a quantitative example of how changes such as restructuring of the health service directly impact on public health surveillance. Such changes have potential risks for information and may affect important data used to inform public health policy.