<p>Macrophages are essential components of the innate immune system and have crucial roles in host defence, tissue homeostasis and inflammation. Embryonic macrophages are specialized populations of macrophages that arise early during development and contribute to tissue organization, immune system development and homeostasis. These cells originate from yolk sac and fetal liver progenitors and colonize various tissues during embryogenesis, becoming long-lived tissue-resident macrophages. In the embryo, macrophages are involved in a wide range of developmental processes, including the clearance of apoptotic cells, regulation of organogenesis and establishment of tissue integrity. They are also pivotal in the early establishment of immune tolerance and in the development of the fetal haematopoietic and immune systems. Plenty of literature covers the role of yolk sac-derived macrophages in adult tissues, whereas less is known about their functions in the embryo itself. This Review highlights our emerging understanding of embryonic macrophages, their origin and their roles in organogenesis and development in mice and humans.</p>