With the aim of characterizing the evolution of the epidemiological profile of respiratory bacterial infections of patients having Cystic Fibrosis (CF), the authors conducted a retrospective analysis about it's incidence and prevalence in 78 CF patients followed at the CF Specialized Centre, Paediatric Department, Santa Maria Hospital, Lisbon, during a 5 years period (1995-1999). Pseudomonas aeruginosa was the most frequently isolated bacteria during the first three years of the study (60-73%), being surpassed by Staphylococcus aureus. However, Pseudomonas aeruginosa always remained the principal agent of chronic colonization (44-59%), with a peak of beginning between 0 and 5 years (34%). A significative increase of the prevalence of intermitent and chronic colonization with Staphylococcus aureus was verified during this five years (48% to 83% and 32% to 54%). The prevalence of isolations of Meticillin Resistant Staphylococcus aureus and of Burkholderia cepacia almost duplicated during this period. The taxes of isolation and chronic colonization with Alcaligenes xylosoxidans raised sharply beyond 1997 (from 3% and 0% in 1996 to 7% and 5% in 1997 and 10% and 7% in 1999). Chronic colonization with Haemophilus influenzae kept a median prevalence of 22%, in spite of an increase in isolations (from 42% to 61%). Fifty five per cent of the patients were chronically colonized by two or more agents. In view of these results, the authors discuss the therapeutic schemes and the measures to limit cross-infection which have been being advocated for CF patients in our centre.