A stem cell niche is a specialized tissue environment that controls the proliferation and differentiation of its resident stem cells. The functions of these structures have been well characterized in adult organisms. In particular, the bone marrow stem cell niche in mammals has been amenable to analysis because of the ability of transplanted hematopoietic cells to home and to recolonize the bone marrow of an irradiated host. Despite clues from adult models, it remains unclear how stem cells become partitioned into appropriate niches during embryonic development. To examine the earliest steps in niche formation, we created an organ culture system to observe the development of primordial germ cells (PGCs), a migratory stem cell population that will eventually give rise to the gametes. Using this assay, we can watch PGCs as they migrate to colonize the developing gonads and can introduce growth factor agonists or antagonists to test the function of proteins that regulate this process. This provides an unprecedented opportunity to identify the cellular and molecular interactions required for the formation of the germ cell niche.