OBJECTIVES: To observe the relative role of individual and group-level antimicrobial selective pressure on subsequent methicillin-resistant Staphylococcus aureus (MRSA) isolation in a university hospital. METHODS: For this purpose, 18 596 patients were included in a retrospective statistical analysis, applying multilevel modelling with discrete time intervals at the lowest level. Individual-level and hospital group variables on antimicrobial exposure and MRSA colonization pressure were collected from computerized databases. RESULTS: The simultaneous hospital group- and individual-level analysis showed individual exposure to fluoroquinolones and collective exposure to penicillins to be associated with MRSA isolation after adjustment for colonization pressure and other potential confounders. CONCLUSIONS: These results support efforts to reduce prescriptions of selected antimicrobial drug classes such as fluoroquinolones and show the added value of multilevel analysis for research on the adverse outcomes of antibiotic prescribing.