The development of induced pluripotent stem cells (iPS cells) has raised the prospect of patient-specific treatments for various diseases. Theoretically, iPS cell technology avoids the limitations of human embryonic stem cells (ES cells), including poor establishment, ethical issues, and immune rejection of allogeneic transplantation. However, the immunogenicity of iPS cells has attracted the attention of researchers, and it remains unclear whether iPS cells and their derivatives will be recognized as a patient's own cells. Even though iPS-derived functional cells have been used in the treatment of some diseases, the process of somatic cell reprogramming and iPS cell differentiation is time-consuming, making it difficult to use iPS cells in acute illness or injury. In recent years, it has been suggested that iPS cells may be used as allografts by establishing an iPS cell bank and HLA matching, providing a novel strategy for the clinical application of iPS cells. This article provides a concise overview of iPS cell immunogenicity, and summarizes published data regarding the application of iPS cells in both autologous and allogeneic transplantation in order to help develop more reliable biotechnical strategies utilizing iPS cells.