Mesenchymal stem cells (MSCs) are of particular interest for the treatment of immune-related diseases because of their immunosuppressive capacities. However, few clinical trials of MSCs have yielded satisfactory results. A number of clinical trials using MSCs are currently in progress worldwide. Unfortunately, protocols and methods, including optimized culture conditions for the harvest of MSCs, have not been standardized. In this regard, complications in the ex vivo expansion of MSCs and MSC heterogeneity have been implicated in the failure of clinical trials. In this review, potential strategies to obtain MSCs with improved immunosuppressive properties and the potential roles of specific immunomodulatory genes, which are differentially upregulated in certain culture conditions, will be discussed.