Microglia are the resident macrophages of the central nervous system (CNS). These pivotal cells arise early during embryonic development and provide both developmental support and immune protection to the brain. In adults, microglia contribute to brain homeostasis and mediate an intriguing interplay between the CNS and the gut microbiota. When dysregulated, microglia are also implicated in numerous neurological disorders, and thus fully understanding their regulation and functions will facilitate rational design of therapies to alleviate these conditions; however it remains unclear how the multiple factors modulating microglial activity are integrated at the organism and cellular levels. In this review, we will discuss recent advances in the understanding of microglial regulation and highlight the key questions that remain to be answered around microglial development, homeostasis and functions.