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BACKGROUND The clinical application of cells and the development of new delivery systems have allowed significant advances in the field of cell therapy and encapsulation in recent years. The ability to combine cells and biocompatible matrices in the encapsulation of cells providing long-term delivery has provides new therapeutic alternatives in the development of new therapies. METHODS A structured search of bibliographic databases was carried out to determine the entire methodology related to cell encapsulation with clinical application. RESULTS Cell encapsulation provides increased retention time in the target tissue improving its therapeutic efficacy. This technology involves the development of a physical barrier (natural or synthetic matrix surrounded by a semipermeable membrane) to isolate and protect cells from the host's immune system maintaining the microenvironment of embedded cells, their viability and their capacity of differentiation, improving their function in vivo, and reducing side effects associated with the use of immunosuppressive therapy. CONCLUSION The purpose of this review is to discuss the different technologies of cell encapsulation and the different materials utilized from both, natural and synthetic origin, and provide an overview of current therapeutic applications of cell encapsulation, as well as, the perspectives for their clinical application including as a novelty the current application in clinical trials.