The healthcare sector in general and hospitals in particular represent a main application area for Data Envelopment Analysis (DEA). This paper reviews 262 papers of DEA applications in healthcare with special focus on hospitals and therefore closes a gap of over ten years that were not covered by existing review articles. Apart from providing descriptive statistics of the papers, we are the first to examine the research purposes of the publications. These research goals can be grouped into four distinct clusters according to our proposed framework. The four clusters are (1) “Pure DEA efficiency analysis”, i.e. performing a DEA on hospital data, (2) “Developments or applications of new methodologies”, i.e. applying new DEAy approaches on hospital data, (3) “Specific management question”, i.e. analyzing the effects of managerial specification, such as ownership, on hospital efficiency, and (4) “Surveys on the effects of reforms”, i.e. researching the impact of policy making, such as reforms of health systems, on hospital efficiency. Furthermore, we analyze the methodological settings of the studies and describe the applied models. We analyze the chosen inputs and outputs as well as all relevant downstream techniques. A further contribution of this paper is its function as a roadmap to important methodological literature and publications, which provide crucial information on the setup of DEA studies. Thus, this paper should be of assistance to researchers planning to apply DEA in a hospital setting by providing information on a) what has been published between 2005 and 2016, b) possible pitfalls when setting up a DEA analysis, and c) possible ways to apply the DEA analysis in practice. Finally, we discuss what could be done to advance DEA from a scientific tool to an instrument that is actually utilized by managers and policymakers.