The aim of this study was to validate the performance of the polymerase chain reaction (PCR) assay for Bordetella pertussis and Bordetella parapertussis in comparison with both culture and serology. The number of samples positive in PCR was 2.4-fold higher than the number of samples positive in culture. In serologically confirmed cases, the sensitivity of PCR and culture depended on the duration of disease and the age of the patient, being less sensitive in older age and later in disease. The sensitivity of the PCR in patients with < 10 days of symptoms was 70%, 50%, and 10% in the age groups < 1 year, 1-4 years, and > or = 5 years, respectively. Evidence suggested that the effect of age on sensitivity may be due to differences in immune responses. The low IgA response in the < 1 year age group may be related to the high number of samples positive in PCR and culture, even late in disease.