This study investigated the accuracy of Primary Health Organisation (PHO) register ethnicity data held within the Waitemata district of Auckland, New Zealand. Ethnicity data of children aged 5–15 years on the National Immunisation Register (NIR) were compared to ethnicity data for those children on the PHO register. NIR data were collected from parents or guardians via a protocol-based informed consent process in the Meningococcal B Immunisation Campaign. Of children recorded as Mäori on the NIR, 62.9% were recorded as Mäori on the PHO register, 23.3% as European and 9.6% as Unknown. Of children recorded as Pacific on the NIR, 77.2% were recorded as Pacific on the PHO register, 9.4% as European, and 6.2% as Unknown. Of children recorded as Asian on the NIR, 81.4% were recorded as Asian on the PHO register, 9.9% as Unknown and 6.0% as European. Of children recorded as European on the NIR, 83.2% were recorded as European on the PHO register and 14.4% as Unknown. These study results indicate that a standardised, systematic and appropriate sector-wide approach is needed for ethnicity data collection, conclude the authors.