Soon after fertilization of the egg and sperm, the zygotic genome is transcriptionally active and drives a series of coordinated cell divisions and gene regulatory programs to establish the basic plant body plan. Although decades of research have deciphered the molecular mechanisms regulating these fundamental processes in animal embryos, much less is known about them in plants. Rather than a lack of interest, this is primarily due to the difficulty in studying early plant embryos because they are small and deeply embedded within maternal tissues. To circumvent these limitations, we have developed molecular biology, microscopy and bioinformatics approaches to characterize the molecular basis of body plan formation at the beginning of plant life.