Drug shortages are a complex and global phenomenon. When a drug cannot be delivered at the moment of patient demand, every stakeholder in the health care system is affected. The aim of this study was to investigate the characteristics, clinical impact, financial impact and management of drug shortages in European hospital pharmacies and identify opportunities for prevention and mitigation of drug shortages in Europe. An online survey was designed based on a review of the literature and interviews and was sent to subscribers of Hospital Pharmacy Europe between June and September 2013. Forty-five percent of respondents (n = 161) indicated that life sustaining or life preserving drugs such as oncology drugs were affected by drug shortages. More than 30% of respondents indicated that drug shortages in Europe were always or often associated with increased costs for hospitals, increased personnel costs and more expensive alternative drugs (n = 161). On the question when information about a drug shortage was obtained, 42% of respondents answered that information from the pharmaceutical company was obtained at the time of no delivery, 50% indicated that information from the wholesaler was obtained at the time of no delivery, while 40% of respondents indicated that information was never or rarely received from the government (n = 161). Fifty seven percent of respondents strongly agreed that an obligation to the producer to notify further shortages could help to solve the problem (n = 161). These results showed that pharmaceutical companies and wholesalers are already involved in the management of drug shortages, while a role is still reserved for the government. Mandatory notification in advance and centralized information can help to reduce workload for hospital pharmacists, will allow early anticipation of drug shortages and will facilitate mitigation of the clinical impact on patients.