Nasopharyngeal aspirates and nasopharyngeal swabs from 177 children exhibiting mild to severe clinical symptoms of whooping cough were tested by the polymerase chain reaction (PCR) and culture for the presence of Bordetella pertussis. In the PCR analysis amplifications of samples prepared with and without DNA extraction were compared. In 26% of samples prepared without DNA extraction, the PCR was found to be inhibited, whereas no inhibition was detected after DNA extraction. Twelve percent (21/177) of the samples were positive in both culture and the PCR, and an additional 49% (87/177) of the samples were positive exclusively in the PCR. Thirty-eight percent (8/21) of culture-positive patients and 63% (55/87) of the patients in whom infection was detected only by PCR had mild or atypical clinical symptoms. Of these groups 26% (5/19) and 50% (39/78), respectively, had been fully vaccinated with three or more doses of diphtheria, tetanus and pertussis vaccine.