Achromobacter xylosoxidans is an emerging pathogen increasingly being isolated from respiratory samples of cystic fibrosis (CF) patients. Its role and clinical significance in lung pathogenesis have not yet been clarified. The aim of the present study was to genetically characterize A. xylosoxidans strains isolated from CF patients by use of randomly amplified polymorphic DNA (RAPD) profiles and to look for a possible correlation between RAPD profiles and the patients' clinical features, such as their spirometry values, the presence of concomitant chronic bacterial flora at the time of isolation, and the persistent or intermittent presence of A. xylosoxidans strains. A set of 106 strains of A. xylosoxidans were typed by RAPD analysis, and their profiles were analyzed by agglomerative hierarchical classification (AHC) and associated with the patient characteristics mentioned above by factorial discriminant analysis (FDA). The overall results obtained in this study showed that (i) there is a marked genetic relationship between strains isolated from the same patients at different times, (ii) characteristic RAPD profiles are associated with different predicted classes for forced expiratory volume in 1 s (FEV1%), (iii) some characteristic RAPD profiles are associated with different concomitant chronic flora (CCF) profiles, and (iv) there is a significant division of RAPD profiles into "persistent strains" and "intermittent strains" of A. xylosoxidans. These findings seem to imply that the lung habitats found in CF patients are capable of shaping and selecting the colonizing bacterial flora, as seems to be the case for the A. xylosoxidans strains studied.Cystic fibrosis (CF) is the most common lethal genetic disease, causing a chronic infection of the respiratory tract, which in turn leads to progressive respiratory deficiency (6,15). Pseudomonas aeruginosa is the most frequently found Gramnegative pathogen in the sputa of patients with CF, while Staphylococcus aureus is the most frequently found Gram-positive one. Recently, new pathogens have also emerged, such as Burkholderia cepacia complex, Stenotrophomonas maltophilia, and Achromobacter xylosoxidans (3,9,18,19,20,24). Although the clinical significance of A. xylosoxidans is not yet clear, it is increasingly being isolated from the sputum cultures of CF patients. Tan et al. (22) found that 2.3% of CF patients had at least 3 positive cultures for A. xylosoxidans during a 6-month period. The U.S. Cystic Fibrosis Foundation's National Patient Registry reported an increase of 4.5%, from 1995 to 2002 (1, 2), in the frequency of isolation of this microorganism from CF patients. Recently, A. xylosoxidans has been considered a nosocomial pathogen, particularly in immunocompromised patients, causing a variety of infections, including bacteremia, meningitis, pneumonia, and peritonitis (8,23,25). Achromobacter spp. are aerobic, nonfermentative, Gram-negative bacilli (5, 7, 21) that are frequently misidentified by routine laboratory tests, thus seriously compromising control ...