Branhamella catarrhalis is increasingly recognized as a lower respiratory tract pathogen, particularly in chronic lung diseases. This project defines a population of patients in whom the dynamics of colonization and infection caused by this organism could be studied. A method employing pulsed field gel electrophoresis (PFGE) of genomic DNA was developed. Twenty-eight patients with bronchiectasis followed prospectively for 26.8 mo (mean) were seen monthly or bimonthly and at the time of a purulent exacerbation. Quantitative bacterial cultures were performed on sputum obtained at each visit. Six of 28 had B. catarrhalis isolated repeatedly. Viable numbers of B. catarrhalis were similar to other bacterial pathogens. Restriction fragment length polymorphism (RFLP) analysis of chromosomal DNA using PFGE was performed on 37 of the 47 isolates recovered. Each patient was colonized by two to four strains with different RFLP patterns. Duration of colonization by the same strain was 2.3 mo (mean). Strain acquisition did not correlate with exacerbation, antibiotic therapy, or season. We conclude that (1) a subset of bronchiectatic patients is colonized with B. catarrhalis, (2) RFLP is a sensitive tool to study strain acquisition, and (3) acquisition and clearance of B. catarrhalis from the respiratory tract is a dynamic process.