There is little found in the published literature regarding the use of endobronchial biopsy (EBB) in children with cystic fibrosis (CF). One concern over the use of the technique may relate to safety, in particular increased risk of bleeding from a hypertrophied bronchial circulation. The aim of this retrospective study was to compare the safety of EBB in children with CF and those with other conditions, the most frequent of which included primary ciliary dyskinesia and recurrent lower respiratory tract infections. Case notes of all children undergoing EBB in our institution between February 2003 and May 2004 were reviewed. EBB was performed during 45 bronchoscopies in 42 CF patients (19 males, group mean age 7.13 +/- 4.48 years) and in 39 controls (20 males, group mean age 6.59 +/- 4.48 years). There were no significant differences between disease groups in the number, type, or severity of complications occurring during or in the first 12 hr after the procedure. We conclude that EBB performed as part of fibreoptic bronchoscopy (FOB) under general anaesthesia can be performed safely in children with CF, when both bronchoscopist and anaesthetist are suitably experienced. Studies of such samples would allow us to determine the early pathological changes in the CF airway and possibly find new treatments to prevent the progression to bronchiectasis and end stage airway destruction.