In patients with cystic fibrosis, infection with Pseudomonas cepacia is associated with poor outcomes. However, the epidemiology of Burkholderia cepacia is still unclear. The aim of this study was to investigate the epidemiology of Burkholderia (Pseudomonas) cepacia colonization among cystic fibrosis patients attending the Verona CF Centre, a large specialized unit to which patients from different parts of Italy are admitted. We used a genome finger-printing system to analyse the nucleotidic structure of B. cepacia isolates from 60 colonized cystic fibrosis patients. Forty-two different finger-printing patterns were identified. Thirty-two patients were colonized by individual B. cepacia strains (53.3%). The remaining 28 subjects were divided into 10 different subgroups, each exhibiting a distinct strain of B. cepacia (46.7%). Nevertheless, direct, person-to-person transmission was evident in only 10 cases (16.7%). The stability up to 12 months, of the B. cepacia colonizing strain was documented in 36 individuals. Consistent with other reports, risk of B. cepacia transmission between cystic fibrosis patients through intimacy or nosocomial contact was found in our study. However, besides low contagiousness, our data suggest that the environmental reservoir of B. cepacia outside the hospital seems to play an important role in B. cepacia infection of our cystic fibrosis population.