Abstract: Microglia, which comprise approximately 10% of total cells in the brain, are the resident immune cells in the central nervous system and contribute to maintaining the brain homeostasis through monitoring their microenvironment (Kettenmann et al., 2011). Recent studies have reported that microglia also regulate neural circuit formation after birth. The functional transition in microglia has been considered to correlate with their morphological changes over time. Although microglial morphologies were found to be modulated by expressions of particular genes, the mechanisms that underlie morphological changes in microglia have not been fully elucidated. Recently, we have reported that FAT atypical cadherin family protein 3 (FAT3) is a novel factor that stabilizes microglial processes regulated by hypoxanthine (Okajima et al., 2020). Since the timing of FAT3 expression coincides with that of microglial morphological changes during the postnatal stage, it is plausible that FAT3 regulates the microglial transition. In this review, we discuss the biological relevance among microglial heterogeneity and transitions. Moreover, we introduce our recent findings that link FAT3 to the aspect of microglial transition and functions during the postnatal stage.