A rapid diagnostic procedure, which is based upon the polymerase chain reaction (PCR) genetic amplification technology, was utilized to establish the presence of Bordetella pertussis in nasopharyngeal washes from children. Overall, 14.7% of 456 specimens were positive by either culture or the rapid assay. Culture and PCR were concordant for 62.7% of positive samples; PCR provided an additional increment of 37.3%. PCR-positive, culture-negative specimens were more likely to be found among older patients with more prolonged illness and previous erythromycin therapy (P < 0.01 for all three comparisons). As a single laboratory assay, PCR should be recognized as the current standard for diagnosis.