Chronic pulmonary infections caused by Pseudomonas aeruginosa, Burkholderia cepacia complex and Staphylococcus aureus are responsible for most of the morbidity and mortality of patients with cystic fibrosis (CF). Little is known about the routes of transmission of these pathogens from environmental or hospital sources to the patients. We hypothesised that strains of P. aeruginosa, B. cepacia complex and methicillin-resistant S. aureus (MRSA) are nosocomially acquired by CF patients. Bacterial isolates were obtained from 164 patients attending the CF Centre of Florence and from the hospital environment and the strains typed using restriction enzymes and pulsed-field gel electrophoresis (PFGE). Seventy (43%) of patients were colonised by P. aeruginosa, 6 (3.6%) by B. cepacia complex, and 11 (7%) by MRSA. Three P. aeruginosa strains were isolated from the sinks of the ward. All the MRSA isolates differed from each other. The analysis of 83 P. aeruginosa strains showed identical genotypes in five pairs of patients, whereas from the six patients infected with B. cepacia complex strains, two patients harboured identical genotypes. These pairs of patients had no contact with each other outside the CF centre and P. aeruginosa genotypes from the hospital environment differed from these clinical isolates, suggesting a possible common source of infection within or outside the centre. The study showed that, despite isolation precautions, a minimal risk of cross-infection still existed in the CF centre and that hygienic standards should be increased to further reduce this risk.