Occurrence of Pseudomonas aeruginosa, Stenotrophomonas (Xanthomonas) maltophilia and Burkholderia (Pseudomonas) cepacia in sputum of cystic fibrosis (CF) patients was demonstrated with a simple and rapid polymerase chain reaction (PCR) technique. The PCR was performed with a set of three primer pairs based on 16S rRNA sequences after sputum preparation with dithiothreitol and NaOH lysis. All three pathogens could be individually detected by the use of this technique. To prevent carry-over contamination, dUTP and uracil-N-glycosylase were included in the reaction. The amplicons were visualized by agarose gel electrophoresis. Sputum culture was performed on all samples. Ninety specimens from CF patients were analysed. The sensitivity for the detection of P. aeruginosa was 37/40 (93%) compared to culture. Bacterial growth of P. aeruginosa was found in three cases, where PCR amplicons were not detected, while PCR was positive in five cases, where culture did not reveal the presence of this bacterium. For this reason, the specificity was 45/50 (90%). For S. maltophilia, the PCR was less sensitive than culture (positive in three of six cases). In our series, B. cepacia was detected by culture in one case and this was also detected by PCR. There were no false-positive PCR results regarding S. maltophilia or B. cepacia. Thus, combined PCR-based detection of these three clinically relevant bacteria in sputum samples from CF patients can be performed by a reliable technique in a relatively simple manner. The present data indicate a high sensitivity and specificity for P. aeruginosa. The lower sensitivity observed for the detection of S. maltophilia in sputum and B. cepacia, as estimated from laboratory strains, may depend on PCR conditions and genetic heterogeneity, respectively. The greatest gains with this method can be made when it is used for the early detection of P. aeruginosa in sputum-producing CF patients.