INTRODUCTION: Recurrent respiratory infections account for most of the morbidity and mortality of cystic fibrosis patients. MATERIALS AND METHODS: The objective was to determine the prevalence of pathogens isolated from lower respiratory tract secretions in cystic fibrosis patients. In this descriptive observational study, data from 69 patients was collected from medical records. RESULTS: The microorganisms that were identified included 36.2% P. aeruginosa, 28.9% S. Aureus, 4.3% K. pneumoniae, 1.5% H. influenzae, 1.5% E. coli, 1.5% S. maltoophilia, and in 27.5% the flora was normal. The prevalence of P. aeruginosa was 83% in patients under two years of age, demonstrating early colonization. CONCLUSION: P. aeruginosa and S. aureus were the most prevalent pathogens; there was also early infection/colonization by P. aeruginosa. This information will contribute to improved therapeutic measures for patients of the Bahia Cystic Fibrosis Reference Center.