Am ajor hurdle in stem cell therapyi st he tumorigenic risk of residual undifferentiated stem cells.T his report describes the design and evaluation of synthetic hybrid molecules that efficiently reduce the number of human induced pluripotent stem cells (hiPSCs) in cell mixtures.T he design takes advantage of Kyoto probe 1( KP-1), af luorescent chemical probe for hiPSCs,a nd clinically used anticancer drugs.A mong the KP-1-drug conjugates we synthesized, we found an exceptionally selective,chemically tractable molecule that induced the death of hiPSCs.M echanistic analysis suggested that the high selectivity originates from the synergistic combination of transporter-mediated efflux and the cytotoxicity mode of action. The present study offers achemical and mechanistic rationale for designing selective,s afe,a nd simple reagents for the preparation of non-tumorigenic clinical samples.