Pluripotent stem cells (PSCs) are a unique population of cells, capable of infinite self-renewal and differentiation into many cell types, making them essential for regenerative medicine, tissue engineering, and drug discovery. With the increasing use of PSCs in clinical trials, it is crucial to accurately assess their differentiation status and understand the diversity within PSC populations. Glycan markers have emerged as key tools for evaluating the undifferentiated state of PSCs, as well as for live and fixed imaging, and for isolating particular cell populations by applying approaches such as fluorescence-activated cell sorting (FACS). This article summarizes the glycan markers used to assess the undifferentiated states of both mouse and human PSCs, which include embryonal carcinoma cells (ECCs), embryonic stem cells (ESCs), and induced pluripotent stem cells (iPSCs). By offering a summary of these markers, we aim to advance our understanding of their role in PSC biology, facilitating further developments in stem cell research and broadening medical applications.