Mesenchymal stem cells or stroma cells (MSCs) were recently proven to play various therapeutic roles when used in clinical trials to control various inflammatory, neoplastic and immunologic diseases in children. Clinical trials show some promising results, particularly in diseases where conventional therapy is still ineffective. However, experimental studies sometimes show conflicting results. This review aims to assess the current therapeutic role of MSCs in the control of several pediatric diseases and elaborate on their future applications by reviewing published studies. A review of published studies on this subject based on Pubmed and Medical Subject Heading databases, with search for all relevant articles focusing on results of clinical trials to evaluate the clinical applications of MSCs. The review includes documentation of positive as well as negative applications of MSCs focused on pediatric diseases. MSCs have important immunosuppressive and antifibrotic effects that need to be employed to help patients with diseases for which no conventional management has proven to be effective. They may be also be used as an adjuvant to conventional therapeutic modalities to consolidate recovery. This review sheds light on the significance of the use of MSCs for the treatment of various pediatric diseases and focuses on promising applications. Most of the reported studies agree about the favorable use of MSCs in various diseases; however, more clinical trials, involving larger numbers of patients, need to be conducted in order to refine the outcome of the therapeutic methods and establish standardized protocols.