Although recent research has indicated an involvement of microglia in synapse remodelling in the normal brain, their precise role in this process is unknown. The synapses of the retinogeniculate system undergo extensive pruning postnatally, and Schafer et al. now find that microglia contribute to this pruning by engulfing and remodelling presynaptic inputs. Interestingly, they show that this process is dependent on upstream neuronal activity and signalling via the phagocytic complement receptor 3 pathway.