The role of pulmonary infection and inflammation in the pathogenesis of destructive lung disease in cystic fibrosis (CF) is undisputed. The use of bronchoscopy and bronchoalveolar lavage (BAL) has demonstrated that these processes may begin early in life and be present in the absence of overt clinical symptoms. Some children diagnosed following newborn screening can be infected with Pseudomonas aeruginosa in infancy. Studies using BAL have demonstrated a relationship between lower airway inflammation and bacterial load in the lungs; however, inflammation may occur in the absence of obvious current infection. BAL has the potential to provide a greater understanding of the pathogenesis of CF lung disease and microbiological surveillance provides the opportunity for early detection and eradication of P. aeruginosa. Lack of standardization inhibits the ability to compare data from different centres and to optimize treatment strategies. This review discusses the recommendations from a workshop held in early 2007 aimed at achieving a standardized approach to BAL in infants and young children with CF.