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Human pluripotent stem cells (hPSCs), represented by embryonic stem (hESCs) and induced pluripotent stem cells (hiPSCs), are attracting increasing attention in various research fields. However, their application in a clinical scenario must overcome an important hurdle given that these cells are potentially tumorigenic. This inherent problem becomes more significant as the number of transplanted cells becomes larger. In this Progress Report, recent findings concerning a novel glycan marker for hPSCs are described, as well as attempts made in relation to its practical application to regenerative medicine. In line with current thinking in the glycoscience field, it is assumed that cellular glycomes are closely related to cell functions. Based on this premise, hESCs and hiPSCs are analyzed by an advanced glycan profiling technology—the high-density lectin microarray. It is found that all human iPSCs derived from different tissular origins show essentially the same glycan profiles, which are typified by several characteristic structural features. In addition, a recombinant lectin probe, rBC2LCN, which shows rigorous specificity to H type 1 and 3 glycan structures, is found to serve as an excellent probe for hPSCs.