Our aims were to describe the epidemiology of Bordetella pertussis infection in Victoria during the last decade and to evaluate surveillance of B. pertussis by comparing notifications with laboratory isolations and hospital diagnoses. Whooping cough was once a leading cause of childhood morbidity and mortality but there was a dramatic reduction in the 1940s because of immunisation. During the last two decades, controversy about the vaccine's toxicity has resulted in waning immunisation rates and outbreaks of the disease. The notification system in Victoria has undergone changes which make interpretation of surveillance data difficult. We compared notifications of B. pertussis with laboratory data from the Royal Children's Hospital and hospital separations with B. pertussis from all hospitals in Victoria. The latter sources revealed epidemic years of infection in 1982, 1985 and 1989. This was not apparent from notifications alone and highlights the importance of using multiple sources of surveillance data. We also found a higher rate of notification from Geelong than rural Victoria and metropolitan Melbourne. The fluctuating incidence of B. pertussis infection in the last decade may reflect changing immunisation practices. Unfounded fears that pertussis vaccine causes serious neurological sequelae have inappropriately influenced individual practice and legislation. The increased notification of B. pertussis in the early 1980s may have reflected the omission of the fourth dose of pertussis vaccine from the Australian schedule in 1979. Surveillance data should be used not only for descriptive epidemiology, but for public health action, and efforts should be made to ensure that immunisation rates remain high.