Microglia, the immune cells of the brain, exhibit interactions with synapses under normal and altered sensory conditions in juvenile mice. Using immunocytochemical electron microscopy, serial section electron microscopy, and two-photon in vivo imaging, the authors characterized these interactions in the visual cortex. During normal visual experience, microglial processes frequently contacted multiple synapse-associated elements, including synaptic clefts, and were surrounded by extracellular spaces. Microglial processes localized to small, transient dendritic spines, which typically shrank over 2 days. When visual experience was altered through light deprivation and reexposure, microglial processes changed their morphology, displayed altered extracellular space distributions, showed phagocytic structures, and more frequently contacted synaptic clefts and enveloped synapse-associated elements. Light deprivation reduced microglial motility and preferentially localized them to larger, persistently shrinking dendritic spines, while light reexposure reversed these behaviors. These findings suggest that microglia may actively contribute to the modification or elimination of specific synaptic structures in the healthy brain, potentially through the regulation of extracellular spaces and phagocytic activities.Microglia, the immune cells of the brain, exhibit interactions with synapses under normal and altered sensory conditions in juvenile mice. Using immunocytochemical electron microscopy, serial section electron microscopy, and two-photon in vivo imaging, the authors characterized these interactions in the visual cortex. During normal visual experience, microglial processes frequently contacted multiple synapse-associated elements, including synaptic clefts, and were surrounded by extracellular spaces. Microglial processes localized to small, transient dendritic spines, which typically shrank over 2 days. When visual experience was altered through light deprivation and reexposure, microglial processes changed their morphology, displayed altered extracellular space distributions, showed phagocytic structures, and more frequently contacted synaptic clefts and enveloped synapse-associated elements. Light deprivation reduced microglial motility and preferentially localized them to larger, persistently shrinking dendritic spines, while light reexposure reversed these behaviors. These findings suggest that microglia may actively contribute to the modification or elimination of specific synaptic structures in the healthy brain, potentially through the regulation of extracellular spaces and phagocytic activities.