Human pluripotent stem cells (hPSCs) such as human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs) are a leading candidate for regenerative medicine/cell therapies because of their capacity for pluripotency and unlimited self-renewal. However, there are significant obstacles preventing the clinical use of hPSCs. A significant safety issues is the presence of residual undifferentiated cells that have the potential to form tumors in vivo. Here, we describe the highly sensitive qRT-PCR methods for detection of residual undifferentiated cells in retinal pigment epithelial (RPE) cells derived from hiPSCs. qRT-PCR using probes and primers targeting LIN28A (LIN28) transcripts can detect residual undifferentiated cell levels as low as 0.002 % in hiPSC-derived RPE cells. We expect this method to contribute to process validation and quality control of hiPSC-derived cell therapy product.