Exploring cell dynamics in living tissues uncovers unknown aspects of organ physiology and pathology. In adult organs, the clearance of defective cells by the immune system is essential for maintaining or restoring homeostasis after damage. We are interested in understanding early embryonic dynamics, a developmental stage in which immune cells are still not formed. Performing quantitative live imaging of zebrafish and mouse embryos at different biological scales, we revealed a tissue clearance program important for embryo survival, that facilitates the correction of errors in early development (Nature 2021). We showed that the surface epithelium of the early embryo eliminates apoptotic stem cells by phagocytic uptake, using similar mechanisms to immune cells. This process involves cellular protrusions that cooperate mechanically to optimize tissue clearance efficiency. We propose that the first tissue formed in development has a protective role for embryonic stem cells. This tissue represents a useful model to explore the dynamics of epithelial phagocytosis in its natural context, and will allow us to evaluate the relevance of these processes for fertility and regeneration.