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In recent years, the incredible interests in mesenchymal stem cells have boosted the expectations of both patients and physicians. Unlike embryonic stem cells, neither their procurement nor their use is deemed controversial. Moreover, their immunomodulatory capacity coupled with low immunogenicity has opened up their allogenic use, consequently broadening the possibilities for their application. In May 2012, Canadian health regulators approved Prochymal, the first mesenchymal stem cells-based drug, for acute graft-versus-host diseases in children who have failed to respond to steroid treatment. The aim of this article is to review the recent advances in mesenchymal stem cells for pediatric diseases. A literature review was performed on PubMed from 1966 to 2013 using the MeSH terms “mesenchymal stem cells”, “clinical trials” and “children”. Additional articles were identified by a hand search of the references list in the initial search. The following categories are described: general properties, mechanisms of action, graft-versus-host diseases, cardiovascular diseases, liver diseases, inflammatory bowel diseases, osteoarticular diseases, autoimmune diseases, type 1 diabetes, and lung diseases. Mesenchymal stem cells, owing to their availability, immunomodulatory properties, low immunogenicity, and therapeutic potential, have become one of the most attractive options for the treatment of a wide range of diseases. It is expected to see more and more clinical trials and applications of mesenchymal stem cells for pediatric diseases in the near future.