Chronic infections of primary ciliary dyskinesia (PCD) airways are strongly associated with morbidity and mortality; however, relatively limited data exist about their microbiology. Therefore, this study was aimed to determine whether there was a correlation between sputum and bronchoalveolar lavage (BAL) microbiology in PCD cases. This was accomplished by comparing the lower airway bacteriology in PCD with the results of sputum samples. We retrospectively analyzed the microbiology of BAL and sputum samples of 114 patients who were diagnosed as PCD and followed up at Hacettepe University Hospital Department of Pediatric Pulmonology. At the time of sampling, patients had no pulmonary exacerbation, and sputum samples were obtained within 3 months of BAL. The mean age of the patients was 13.5 +/- 4.3 (range 3-21 years) years. Microbiological analysis revealed microorganisms in 47.4% of sputum samples and in 63.2% of BAL samples. In both BAL and sputum samples, Haemophilus influenzae was the most frequent pathogen, followed by Streptococcus pneumoniae. Pseudomonas aeruginosa was detected more frequently in children at older ages. Aspergillus spp. was detected only in BAL samples. The microbiological yield of BAL samples was higher than the sputum samples. There was no significant correlation between the patient age and positive microbiology of BAL and sputum samples. In PCD patients, there was a higher microbiological yield in BAL samples than the sputum samples. Therefore, we conclude that negative sputum microbiology results should be evaluated cautiously, as the rate of bacterial and fungal yield was higher in BAL specimens. The results of this comparative study support the view that sputum cultures do not always reflect the lower airway microbiology in the management of pulmonary disease in PCD.