Mesenchymal stem cells (MSCs) are important clinical applications in treating immune disorders due to their multipotency, immunosuppressive properties by production of cytokines. However, the majority of studies rely on an in vitro cell expansion phase, and the properties of MSCs in vivo are still unknown, because there is no specific marker for MSCs. The purpose of this review is to provide an update on our knowledge of MSCs isolation and their immunosuppressive properties, focusing on bone marrow-derived MSCs.