Background Infection and inflammation are important in the pathogenesis of bronchiectasis. However, there are few published data describing the lower airway microbiology and cellularity in children. Methods Children with non-cystic fibrosis (CF) bronchiectasis who underwent bronchoalveolar lavage (BAL) within 4 weeks of diagnosis were identified by a retrospective patient-record review. The effects of infection (?10 5 colony-forming units of respiratory bacteria/ml; or detectable Pseudomonas aeruginosa; mycobacteria, fungi, mycoplasma, or respiratory viruses) on airway cellularity and the impact of age, gender, indigenous status, immune function, radiographic involvement and antibiotic usage on infection risk were evaluated. Results Of 113 children [median age 63 months (IQR 32-95)] with newly diagnosed bronchiectasis, 77 (68%) had positive BAL cultures for respiratory bacterial pathogens. Haemophilus influenzae was most commonly detected, being present in 53 (47%) BAL specimens. P. aeruginosa was found in just 7 (6%) children, five of whom had an underlying disorder, while mycobacterial and fungal species were not detected. Respiratory viruses were identified in 14 (12%) children and Mycoplasma pneumoniae in two others. Overall, 56 (49.5%) children fulfilled our definition of a lower airway infection and of these, 35 (63%) had more than one pathogen present. Compared to children without infection, children with infection had higher total cell counts (610 vs. 280 �10 6/L), neutrophil counts (351 vs. 70 �10 6/L), and neutrophil percentages (69% vs. 34%). Age at diagnosis was most strongly associated with infection. Conclusions BAL microbiology of children with newly diagnosed bronchiectasis is dominated by H. influenzae. In the absence of CF, isolation of P. aeruginosa may suggest a serious co-morbidity in this group. Airway neutrophilia is common, especially with higher bacterial loads. Copyright � 2011 Wiley Periodicals, Inc.