Hematopoietic stem cells (HSCs) constitute a pool of very rare cells able to self-renew, proliferate, and/or differentiate to all the blood cell lineages during the life span. The first murine adult transplantable HSCs appear in the intraembryonic aorta-gonad-mesonephros region at embryonic day (E) 10.5. After E11, these HSCs are thought to seed the liver and then the bone marrow just before birth. So far, many questions concerning the origin, properties, and functionality of these HSCs have not been answered. To address these issues, it is necessary to isolate and purify them. One of the major problems concerning embryonic HSCs, as compared with their adult counterpart, is that they share many markers with endothelial cells at this early stage of development, making their purification very difficult. This review presents the best methods (sorting based on specific antibody staining, transgenic markers, cell cycle) for the purification and isolation of HSCs from the mouse embryo.