BACKGROUND Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen in cystic fibrosis (CF), with increasing incidence in recent years. We examined the association between bacterial colonization in the sputum (MRSA with or without pseudomonas (PA)) and computed tomography (CT) scores in CF patients. METHODS MRSA patients were divided according to PA status based on at least three consecutive sputum cultures; controls were patients without MRSA (with or without PA), matched for gender and age at CT. Clinical data and CT scores were compared between groups. RESULTS Of 33 patients with MRSA, 14 had no PA (MRSA + PA-) and 19 had also PA (MRSA + PA+). MRSA + PA- and MRSA + PA+ patients had CT scores similar to their controls PA+ (38.25 ± 20.18 vs. 32.22 ± 18.74, P = .4, and 41.88 ± 18.18 vs. 45.33 ± 11.5, P = .4, respectively). Although MRSA + PA- had worse CT scores than their matched PA- controls, their mean FEV1 values were similar. CONCLUSIONS Colonization with MRSA in CF is associated with structural CT changes at least similar to those in PA. A cause and effect relationship cannot be established. The current findings call for a larger study assessing longitudinally the impact of MRSA acquisition and eradication protocols.