A retrospective case-control study of 12 patients positive for Stenotrophomonas maltophilia and 24 age-sex-matched controls revealed that in the year prior to initial isolation, colonised patients spent more days in hospital and received more days of oral ciprofloxacin, intravenous anti-pseudomonal antibiotics, and nebulised aminoglycosides. They were also more likely to have grown Pseudomonas aeruginosa at some time in the past, despite there being no difference in current chronic infection with this organism. The role of anti-pseudomonal antibiotics in promoting Stenotrophomonas maltophilia colonisation in cystic fibrosis is discussed.