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Advanced therapies are a group of medicines for human use based on gene therapy, somatic cell therapy or tissue-engineering. In this paper we present some general basic concepts, describe the most promising strategies and summarize the results of a variety of clinical trials for a significant group of monogenic inherited diseases. Major emphasis is placed on ex vivo gene therapy approaches for diseases of the hematopoietic system, since these corresponded to pioneering treatments that have guided research in this field. We also highlight some examples of successful in vivo gene therapy and point out the contribution of somatic cell therapy and tissue engineering to the group of rare skin diseases. We aim to provide an overview of the state of the art of advanced therapies in rare diseases and highlight some of the cutting-edge technologies under development that can provide more effective and safer treatments in the future.