We have developed a high-density lectin microarray and performed a comprehensive and facile glycan analysis of 114 types of human iPS cells generated from five different somatic cells, and compared their glycomes with those of ES cells (9 cell types). We found that somatic cells with originally distinct glycan profiles acquire those similar to ES cells upon induction of pluripotency. The increased expression of α2-6sialylation, α1-2fucosylation, and type1 LacNAc was found to be the characteristic glycan structural features common to human ES/iPS cells. Finally, we found that rBC2LCN with specificity to the glycans containing the above two characteristics (H type1/3: Fucα1-2Galβ1-3GlcNAc/GalNAc) reacts specifically with undifferentiated cells, which should be a useful probe to discriminate pluripotency.