Objectives: To assess the effectiveness of three, four and five doses of acellular pertussis vaccine against pertussis notification for children aged 1 - < 4 years and 5 - < 12 years, and the effectiveness of three doses of acellular pertussis vaccine against pertussis hospitalisation for children aged 1 - < 4 years. Design, setting and participants: A population-based retrospective study of children aged 1 - < 12 years residing in Queensland, Australia, during 2009 and 2010. Routinely collected notification, hospitalisation, testing and vaccination data were used to describe notification rates and testing patterns and to assess vaccine effectiveness (VE) by the screening method. Main outcome measures: VE against pertussis notification for children aged 1 - < 4 years and 5 - < 12 years, by birth year, and VE against pertussis hospitalisation for children aged 1 - < 4 years. Results: 1961 notifications and 29 hospitalisations were included in the VE calculations. VE point estimates against pertussis notification and hospitalisation in children aged 1 - < 4 years were similar in 2009 and 2010, and ranged between 83.5% and 89.4%. VE point estimates against notification among children aged 5 - < 12 years were between 71.2% and 87.7% in 2009, and between 34.7% and 70.3% in 2010. The numbers of pertussis tests performed for children, particularly polymerase chain reaction (PCR) tests, increased between 2009 and 2010. Conclusions: Acellular pertussis vaccine provided good protection within the first years of priming, but this waned as age increased. Changes in pertussis testing behaviour, because of increases in PCR use and awareness, may have contributed to increased pertussis notification rates and lower estimates of VE against notification owing to identification of milder disease.