Bronchopulmonary infection in cystic fibrosis (CF) patients is associated with chronic progressive lung disease and episodes of acute exacerbation. Infection is predominantly caused by bacteria, although infections with viruses, mycoplasma and fungi may play undervalued roles. Bacteria commonly isolated from CF sputum include Staphylococcus aureus, Haemophilus influenzae and Pseudomonas aeruginosa. Colonisation of the airways by mucoid, alginate-producing variants of P. aeruginosa is recognised as a major cause of pulmonary deterioration. In addition, there is now considerable concern relating to the clinical consequences of colonisation and cross-infection with P. cepacia. This review discusses the microbiology of CF focussing on the pathogenesis and epidemiology of P. aeruginosa and P. cepacia.