BACKGROUND: In cystic fibrosis (CF), chronic infection of the airways with Achromobacter xylosoxidans have become more frequent. The pathogenic role of this is yet unclear. METHODS: A retrospective case-control study of all patients chronically infected with A. xylosoxidans for at least 3 years. 15 patients (6 males) with chronic A. xylosoxidans infection were matched by age, FEV(1) and body mass index z-score to 15 controls (7 males) at the time of establishment of chronic infection. Clinical parameters of the groups were compared from the time of establishment of chronic infection until spring 2006, giving a follow-up time of 3-11 years. Chest X-rays taken 3 years prior to establishment of chronic infection and after 3 years of chronic infection were compared using a modified Brasfield score. Finally, strains from individual patients were analysed using PFGE to investigate possible cross-infection. RESULTS: The median slope of decline of FEV(1) in the case group changed from +3.1% to -0.5% predicted/year (p<0.002). In the control group, median slope of decline in FEV(1) changed from +1.5% to -0.4% predicted/year (n.s.). Median slope of decline in FVC in the case group changed from +3.5% to -0.5% predicted/year (p<0.002). In the control group, median slope of decline in FVC changed from +1.7% to +0.4% predicted/year (n.s.). No significant difference in the slopes of decline of FEV(1) or FVC was found between the case group and the control group at either time. Change in BMI z-score was calculated for each group before and during chronic infection. No difference was found between the groups at any time or within a group. Specific antibodies against A. xylosoxidans were measured in patients with chronic infection. Patients with rapidly increasing antibody levels showed significantly faster deterioration in FEV(1) (p<0.05) and FVC (p<0.02). Chest X-ray scores increased in 6 of 10 chronically infected patients and in 3 of 10 controls (n.s.). Eight patients harboured a common A. xylosoxidans strain, indicating either cross-infection or a common source. CONCLUSION: A. xylosoxidans may lead to a decline in lung function in a subgroup of chronically infected CF patients characterised by a rapid increase in specific precipitating antibodies. Cross-infection may possibly occur.