In this study, sputum samples collected from cystic fibrosis patients with preliminary diagnosis of pulmonary infection were evaluated for the presence of bacteria belonging to Burkholderia cepacia complex by commercial phenotypic systems and recA polymerase chain reaction (PCR). A total of 85 patients ages between 5-30 years (mean age: 12.8 years) were included to the study with female/male ratio of 44/41. The mostly isolated bacteria from 85 sputum samples were found as Staphylococcus aureus (55.3%), Pseudomonas aeruginosa (48.2%) and Haemophilus influenzae (15.3%), whereas B. cepacia complex was phenotypically identified from two (2.3%) out of the samples. However only one was confirmed by PCR and typed as Burkholderia multivorans by restriction fragment lenght polymorphism method. This study emphasizes the importance of molecular methods as confirmatory tests for accurate identification of B. cepacia complex.