OBJECTIVE: To assess the discriminatory power of two genotypic and two phenotypic techniques by analysis of Pseudomonas aeruginosa sputum isolates obtained with long term intervals from 29 independent cystic fibrosis (CF) patients. METHODS: Fifty-eight strains of P. aeruginosa were subjected to serotyping and pyocin production was assessed. Arbitrarily primed polymerase chain reaction (AP PCR) and pulsed-field gel electrophoresis (PFGE) were applied in order to detect genetic polymorphisms. RESULTS: From the results of different typing techniques, it appeared that the numbers of separate types varied between 11 and 43, and the percentage of identical P. aeruginosa pairs from individual patients varied between 51% and 72%, depending on the test system used. AP PCR and PFGE displayed enhanced resolution when compared to serotyping and pyocin typing; both DNA typing techniques generated concordant results, although differences in resolution are apparent. This results in 15% discordance, which may be the result of differences in the definitions of (sub)clonal relatedness as applied for AP PCR and PFGE, respectively. CONCLUSIONS: Molecular typing techniques are superior to phenotyping where P. aeruginosa is concerned. AP PCR is a fast and useful technique for determining clonality among P. aeruginosa strains from chronically colonized CF patients. It is clear, however, that the interpretation of data and comparative analysis of PFGE and AP PCR results necessitates additional (international) standardization and the development of practical guidelines.