Mesenchymal stromal/stem cells (MSCs) possess the ability to self-renew and differentiate into other cell types. Because of their anti-inflammatory and immunomodulatory abilities, as well as their more ready availability compared to other stem cell sources, MSCs hold great promise for the treatment of many diseases, such as haematological defects, acute respiratory distress syndrome, autoimmunity, cardiovascular diseases, etc. However, immune rejection remains an important problem. MSCs are considered to have low immunogenicity, but they do not have full immunological privilege. This review analyzes and discusses the safety of MSCs from the perspective of their immunogenicity, with the aim of providing a reference for future research and clinical application.