Most cancers are detected when patients present with symptoms, and at that point the disease is usually quite advanced and often not curable. Therefore, new biomarkers are needed for detection and therapy. The recent success of using monoclonal antibodies against nonprotein gangliosides for the treatment of high-risk neuroblastoma provides an incentive to search for new glycan-targeted immunotherapies for cancer using markers found through glycomic analysis as targets. Since more than 85% of cell surface components are glycosylated, glycomic analysis is useful to probe systematically the cancer cell surface, in search for novel glycoproteins and glycolipids. Furthermore, cancer cells tend to dedifferentiate and express many oncofetoproteins, since human embryonic stem cells (ESCs) are derived from epiblast of embryo, representing the early stage of normal embryonic development before gastrulation. Unique ESC surface markers are likely to be found in cancer cells, but not in normal mature tissues. Moreover, stem cells and cancer cells share several common features in related regulatory mechanisms and signaling pathways. Thus, identification of the cancer stem cells in cancer and definition of the glycoproteomic changes that accompany their transformation are important for the development of strategies for early detection and treatment of cancer.