SignificanceA main requisite for organogenesis is the integration of vascular networks, which not only deliver oxygen and nutrients but also serve instructive roles in organ patterning that determine how organs develop into their final structure and function in the adult. Our previous work showed that vascularization is essential to induce formation of the primitive cord structures that give rise to the seminiferous tubules of the adult testis. Here we show that fetal macrophages are required to remodel the vasculature and refine organ compartments during differentiation of the gonad. This study reveals an underappreciated and likely vital role for macrophages in fetal organogenesis that may be relevant to the development of many organs.