Objectives Pseudomonas aeruginosa (Pa) is the predominant pathogen affecting patients with cystic fibrosis(CF). Antibiotic therapy aimed at eradicating Pa after early lung infection have played a major role in the increasing median survival of CF patients. Method We examined the demographic, clinical and microbiological data of 146 CF patients with firstly Pa isolation from all 630 CF patients following at Hacettepe University Department of Pediatric Pulmonology and evaluated eradication protocols. Results The mean age of the patients was 71.5 months(2–348 months) at first isolation; and 133 patients had symptoms. S. aureus was the most common co-pathogen(n = 64) and malnutrition was the most common comorbid condition(n = 44). The most common treatment choices are two weeks of intravenous ceftazidim-amikacin in severe exacerbation or 3 months of inhaled gentamycin with 3 weeks of oral ciprofloxacin combination in mild exacerbation and asymptomatic patients. We noticed eradication in 47 patients(32%), intermittan colonization in 42 patients(28%) and chronic colonization in 57 patients(40%). FEV1 decline was statistically significant in intermittan colonization and chronic colonization (p = 0.006). The patient's age of older than two years or having symptoms at the first isolation negatively affects the success of treatment. Conclusion It is now generally accepted that early antibiotic treatment of the initial growth of Pa can eradicate the organism, prevent or delay the development of chronic colonization. Relative low success rate of the eradication may be explained because of no reimbursement of inhaled tobramycin and colistin for eradication therapy in our country.