Background A hospitalization phase represents a challenge to medication safety especially for multimorbid patients as acute medical needs might interact with pre-existing medications or evoke adverse drug effects. This project aimed to examine the prevalence and risk factors of potentially inappropriate medications (PIMs) and medication combinations (PIMCs) in the context of hospitalizations. Methods Analyses are based on claims data of patients (≥65 years) with basic mandatory health insurance at the Helsana Group, and on data from the Hirslanden Swiss Hospital Group. We assessed PIMs and PIMCs of patients who were hospitalized in 2013 at three different time points (quarter prior, during, after hospitalization). PIMs were identified using the PRISCUS list, whereas PIMCs were derived from compendium.ch. Zero-inflated Poisson regression models were applied to determine risk factors of PIMs and PIMCs. Results Throughout the observation period, more than 80% of patients had at least one PIM, ranging from 49.7% in the pre-hospitalization, 53.6% in the hospitalization to 48.2% in the post-hospitalization period. PIMCs were found in 46.6% of patients prior to hospitalization, in 21.3% during hospitalization, and in 25.0% of patients after discharge. Additional medication prescriptions compared to the preceding period and increasing age were the main risk factors, whereas managed care was associated with a decrease in PIMs and PIMCs. Conclusion We conclude that a patient’s hospitalization offers the possibility to increase medication safety. Nevertheless, the prevalence of PIMs and PIMCs is relatively high in the study population. Therefore, our results indicate a need for interventions to increase medication safety in the Swiss healthcare setting.