The collection of sputum for microbiological examination in young cystic fibrosis patients can be very difficult. However, a knowledge of bacterial flora colonizing the patient's airways is of paramount importance for proper antimicrobial therapy. It is also known that cystic fibrosis patients colonized by Pseudomonas species have a poorer prognosis than Pseudomonas-negative patients. Noninvasive ways of diagnosing airway inflammation that require only minimal cooperation of the patient might yield new possibilities for early detection of airway colonisation. The breath condensate method as a noninvasive diagnostic technique seems especially appropriate for use in children. Therefore, the aim of this study was to evaluate whether the breath condensate method could be used for detection of Pseudomonas species in children with cystic fibrosis. In total, 32 breath condensate and seven sputum samples were obtained from 13 cystic fibrosis patients with Pseudomonas aeruginosa- or Burkholderia cepacia-positive sputum culture (20 samples were obtained during forced expiration). PCR for combined detection of Pseudomonas aeruginosa, Stenotrophomonas maltophilia, and Burkholderia cepacia was performed. PCR results of all breath condensate samples were negative for Pseudomonas aeruginosa, Stenotrophomonas maltophilia, or Burkholderia cepacia while all sputum sample results were positive. A minimum DNA quantity of 10 fg could be detected in dilution series of the positive control group. We conclude that the breath condensate method cannot be used as a tool for detection of Pseudomonas species.