Methods for growing whole mouse embryos in vitro have been greatly improved in the last two decades. The present technology enables embryos to develop remarkably close to what can be achieved in vivo from the pre-gastrula to the early organogenesis stages. The ability to grow whole embryos for a substantial period outside the uterine environment offers a unique opportunity to observe the progression of development, and permits the performance of direct manipulation on the embryo. Experiments combining whole embryo culture and micro-manipulation have led to the discovery of new information on lineage differentiation, tissue interaction and morphogenetic mechanisms that are associated with the establishment of the fetal body plan.