Previous studies have suggested that penicillin-resistant pneumococcal isolates (especially those with MIC > 1 microgram/mL) usually are clonally related. To test this hypothesis, the molecular epidemiology of 29 clinical isolates of penicillin-resistant pneumococci (of which 83% were also resistant to either cefotaxime or ceftriaxone) collected in central Taiwan was investigated by pulsed field gel electrophoresis. Twenty-seven distinct patterns were identified. Our results indicate that an increase in penicillin-resistant S. pneumoniae between April 1993 and June 1994 in central Taiwan is not due to the clonal dissemination of a limited number of epidemic strains.