OBJECTIVES: The aim of this study was to determine the temporal relation between the use of antibiotics and alcohol-based hand rubs (ABHRs) and the incidence of methicillin-resistant Staphylococcus aureus (MRSA) and Clostridium difficile. METHODS: An interventional time-series analysis was performed to evaluate the impact of two promotion campaigns on the consumption of ABHRs and to assess their effect on the incidence of non-duplicate clinical isolates of MRSA and C. difficile from February 2000 through September 2006. This analysis was combined with a transfer function model of aggregated data on antibiotic use. RESULTS: Consumption of ABHRs correlated with MRSA, but not with C. difficile. The final model demonstrated the immediate effect of the second hand hygiene promotion campaign and an additional temporal effect of fluoroquinolone (time lag, 1 month; i.e. antibiotic effect delayed for 1 month), macrolide (lag 1 and 4 months), broad-spectrum cephalosporins (lag 3, 4 and 5 months) and piperacillin/tazobactam (lag 3 months) use. The final model explained 57% of the MRSA variance over time. In contrast, the model for C. difficile showed only an effect for broad-spectrum cephalosporins (lag 1 month). CONCLUSIONS: We observed an aggregate-level relation between the monthly MRSA incidence and the use of different antibiotic classes and increased consumption of ABHR after a successful hand hygiene campaign, while no association with ABHR use was detected for C. difficile.