The recent isolation and characterization of mesenchymal stem cells (MSCs) in dental tissues constitutes a major step forward in the development of new treatment strategies. MSCs are essential for dental pulp repair and the success of regenerative endodontic procedures. It is important to understand that immune cells and cytokines can affect stem cell function, which can impact their healing potential. On the other hand, stem cells are immunoprivileged and have the ability to modulate immune and inflammatory responses, which can be utilized to improve treatments outcome. This review addresses both aspects of this interaction and suggests that any change on both sides can tip the balance in favour of either persistence of inflammation or healing. Finally, the therapeutic relevance of the interaction between MSCs and immune system relative to current treatments is discussed, and future research and treatment perspectives are suggested.