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Artificial intelligence is a broad field that comprises a wide range of techniques, where deep learning is presently the one with the most impact. Moreover, the medical field is an area where data both complex and massive and the importance of the decisions made by doctors make it one of the fields in which deep learning techniques can have the greatest impact. A systematic review following the Cochrane recommendations with a multidisciplinary team comprised of physicians, research methodologists and computer scientists has been conducted. This survey aims to identify the main therapeutic areas and the deep learning models used for diagnosis and treatment tasks. The most relevant databases included were MedLine, Embase, Cochrane Central, Astrophysics Data System, Europe PubMed Central, Web of Science and Science Direct. An inclusion and exclusion criteria were defined and applied in the first and second peer review screening. A set of quality criteria was developed to select the papers obtained after the second screening. Finally, 126 studies from the initial 3493 papers were selected and 64 were described. Results show that the number of publications on deep learning in medicine is increasing every year. Also, convolutional neural networks are the most widely used models and the most developed area is oncology where they are used mainly for image analysis. [ABSTRACT FROM AUTHOR]