Induced Pluripotent Stem Cells (IPSCs) open the great possibility to employ patient's own tissue to the previously incurable diseases. However these cells can be used in cell therapy only if they are not rejected when transplanted back into the syngeneic host. We found that the injection of iPSCs derived from different ages of mice into syngeneic C57BL/6 mice produced teratoma and was not rejected. Then we cultured iPSCs and myeloid differentiated iPSCs in three-dimensional porous scaffold and transplanted to C57BL/6 mice and BALB/C mice. After transplantation, we could observe the cell density inside the scaffold increased rapidly in syngeneic mice compared to the allogeneic mice indicating the favorable conditions supporting the growth of iPSCs in vivo. Unlike the allogeneic counterpart, we could not observe few infiltrating T cells inside the scaffold of syngeneic mice. These results contribute to the optimistic view of iPSCs for regenerative medicine in near future.