Hematopoietic stem cells (HSCs) are maintained in a particular microenvironment termed a "niche." Within the niche, a number of critical molecules and supportive cell types have been identified to play key roles in modulating adult HSC quiescence, proliferation, differentiation, and reconstitution. However, unlike in the adult bone marrow (BM), the components of stem cell niches, as well as their interactions with fetal HSC during different stages of embryonic development, are poorly understood. During embryogenesis, hematopoietic development migrates through multiple organs, each with different cellular and molecular components and hence each with a potentially unique HSC niche. As a consequence, isolating fetal HSC from each organ at the time of hematopoietic colonization is fundamental for assessing and understanding both HSC function and their interactions with specific microenvironments. Herein, we describe methodologies for harvesting cells as well as the purification of stem and progenitors from fetal and newborn liver, spleen, and BM at various developmental stages following the expansion of hematopoiesis in the fetal liver at E14.5.