The efficient and selective removal of apoptotic cells is an important feature of tissue development, homeostasis and pathology. In the nervous system, synapses and distal axons are selectively eliminated as part of the remodelling that underpins development and pathology, through a process that has some features in common with apoptotic cell removal. Components of the complement cascade are implicated in the efficient removal of apoptotic cells outside the nervous system, and recent evidence suggests that the complement components C1q and C3 have a role in the selective tagging of supernumerary synapses in the developing visual system and in their efficient removal by as yet unidentified cells.