Much attention has been focused on human pluripotent stem cells (hPSCs) due to their potential as cell sources in regenerative therapies. Especially in the area of cardiac regenerative medicine, which is challenged by organ shortage, transplantation of human induced pluripotent stem cells (hiPSC)-derived cardiomyocytes has potential to treat many patients with severe heart failure. However, to achieve transplantation of hiPSC-derived cardiomyocytes, removal of contaminated immature cells with high accuracy is essential to eliminate the risk of teratoma formation caused by residual undifferentiated hiPSCs. Peptide vaccination is well-known as an effective anticancer immunotherapy because of selective cellular cytotoxicity. To establish immunological elimination of contaminated immature hiPSCs, we identified glypican-3 (GPC3) as a pluripotent state-specific carcinoembryonic antigen. Immunostaining showed that hiPSCs expressed GPC3, especially in pluripotent states. Undifferentiated hiPSCs were rejected by cytotoxic T cell (CTL) clones sensitized with HLA-class I-restricted GPC3 peptides. These results indicate that GPC3-specific CTLs can prevent hiPSC-derived tumorigenesis, which may occur by contamination by undifferentiated cells. Our results indicate that GPC3 works as a pluripotent state-specific immunogenic antigen in hiPSCs. These results show the applicability of GPC3-mediated immunotherapy to ensure safety in regenerative medical procedures using hiPSCs.