Mesenchymal stem cells are present within the bone marrow cavity and serve as a reservoir for the continuous renewal of various mesenchymal tissues. Recent studies suggest that mesenchymal stem cells modulate immune reactions in vitro and escape from immune surveillance in vivo. We provide herein a discussion of issues including the current research progress on the in vitro interactions of mesenchymal stem cells with multiple subsets of immune cells (dendritic cells, T cells, B cells and NK cells), in vivo transplantation outcomes, the possible underlying mechanisms, future research directions as well as potential clinical implications.