Glycosphingolipids are important components of the outer layer of the plasma membrane in the majority of eukaryotic cells. Specifically, gangliosides are sialic acid‑containing glycosphingolipids that participate in cell‑cell recognition, adhesion, proliferation, differentiation and signal transduction, and are integral components of cell surface microdomains and lipid rafts. Stem cells are defined functionally as cells that have the capacity to self‑renewal and differentiate to generate various cell types. Due to different synthesis patterns and locations of gangliosides, they have been used as molecular markers of stem cells. The current review describes the presence of gangliosides in various types of mouse stem cells, including pluripotent stem cells (embryonic stem cells and induced pluripotent stem cells) and neural stem cells, and the functional roles of gangliosides in various processes, including cell proliferation and neural differentiation. Thus, this review will aid the understanding of gangliosides patterns and functions in mouse stem cells, and outline markers for the identification of stem cells.