Microglia are the macrophages in the brain and are the only subset of immune cells in the brain parenchyma. Previous studies about microglia have been mainly focusing on their protection of the brain from pathogen invasions and their protective or toxic roles in the degenerative diseases. In contrast to the abundant knowledge of their pathological roles, little is known about the physiological functions of microglia. Interestingly, recent studies have revealed that microglia play key roles in both the developmental and the mature healthy brains. During the neural development, microglia regulate neurogenesis as well as neuronal death and play key roles in synapse pruning. In the mature healthy brains, microglia detect and regulate neuronal activities. In this review, we will focus on the most recent discoveries of microglial functions in the healthy brain.