Success in the derivation of human embryonic stem cell (hESC) lines has opened up a new area of research in biomedicine. Human ESC not only raise hope for cell replacement therapies but also provide a potential novel system to better understand early human normal development, model human abnormal development and disease, and perform drug-screening and toxicity studies. The realization of these potentials, however, depends on expanding our knowledge about the cellular and molecular mechanisms that regulate self-renewal and lineage specification. Here, we briefly highlight the potential applications of hESC and review how flow cytometry has contributed to the initial characterization of both undifferentiated hESC cultures and hematopoietic development arising from hESC. We envision that a combination of state-of-the-art technologies, including cytomics, proteomics and genomics, will be instrumental in moving the field forward, ultimately lending invaluable knowledge to research areas such as human embryology, oncology and immunology.