Due to their lower rate of adverse events, acellular pertussis vaccines (diphtheria-tetanus-acellular pertussis; DTaP) replaced whole cell vaccines (diphtheria-tetanus-whole cell pertussis; DTwP) in many developed countries during the 1990s. DTaP became available in Queensland, Australia, in 1996 and replaced DTwP for publicly funded primary course immunizations delivered at ages 2 months, 4 months, and 6 months in March 1999. This meant children born in 1998 could receive a primary course consisting of only DTwP, only DTaP, or a mixed schedule. Similar to North America,1 Australia is experiencing a sustained pertussis epidemic,2 with the highest incidence rates in Queensland during 2011 in children aged 6 to 11 years. The recent changes in pertussis epidemiology may be related to the shift from DTwP to DTaP. To test this hypothesis, we compared pertussis reporting rates by primary course vaccination in the 1998 birth cohort.