Recent bronchoscopy studies using assays to measure inflammation and molecular typing techniques have facilitated an increased understanding of the early events that occur within the lungs of young children with cystic fibrosis and provided additional insights into the natural history of lung disease in children. In 2000, the US CF National Patient Registry data showed that among 1000 infants <2 years of age, the first bacterial pathogens detected are Haemophilus influenzae, Staphylococcus aureus, and Pseudomonas aeruginosa and the prevalence of these pathogens in these young infants are 19%, 42%, and 29%, respectively. In addition, 7% harbour Stenotrophomonas maltophilia and <1% harbour Burkholderia cepacia complex. Several investigators have performed bronchoscopy studies on young infants to further examine the natural history of lung disease. In one such study of 40 CF infants, 65%, 63% and 70% of children at 1, 2, and 3 years of age harboured at least one CF pathogen. H. influenzae was most common (38%) in infants at 1 year of age, and S. aureus was most common in 2 (37%) and 3 (36%) year olds. P. aeruginosa increased from 18% at 1 year of age to 33% at 3 years of age and was usually present in high numbers, i.e., > or =10(5) CFU/ml of BAL fluid. Investigators have studied the microbiology of young CF infants using specimens derived from the upper airway (deep throat) compared with the lower airway (broncheoalveolar lavage specimens) to determine if the upper airway is predictive of pathogens in the lower airway. In general, these studies have shown that a negative oropharyngeal culture indicated that isolation of P. aeruginosa from the lower airway was unlikely, but a positive culture did not predict lower airway infection. Similar findings were noted for H. influenzae and S. aureus.