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Precise synapse elimination is essential for the establishment of a fully developed neural circuit during brain development and higher function in adult brain. Beyond immune and nutrition support, recent groundbreaking studies have revealed that phagocytic microglia and astrocytes can actively and selectively eliminate synapses in normal and diseased brains, thereby mediating synapse loss and maintaining circuit homeostasis. Multiple lines of evidence indicate that the mechanisms of synapse elimination by phagocytic glia are not universal but rather depend on specific contexts and detailed neuron–glia interactions. The mechanism of synapse elimination by phagocytic glia is dependent on neuron-intrinsic factors and many innate immune and local apoptosis-related molecules. During development, microglial synapse engulfment in the visual thalamus is primarily influenced by the classic complement pathway, whereas in the barrel cortex, the fractalkine pathway is dominant. In Alzheimer's disease, microglia employ complement-dependent mechanisms for synapse engulfment in tauopathy and early β-amyloid pathology, but microglia are not involved in synapse loss at late β-amyloid stages. Phagocytic microglia also engulf synapses in a complement-dependent way in schizophrenia, anxiety, and stress. In addition, phagocytic astrocytes engulf synapses in a MEGF10-dependent way during visual development, memory, and stroke. Furthermore, the mechanism of a phenomenon that phagocytes selectively eliminate excitatory and inhibitory synapses is also emphasized in this review. We hypothesize that elucidating context-dependent synapse elimination by phagocytic microglia and astrocytes may reveal the molecular basis of synapse loss in neural disorders and provide a rationale for developing novel candidate therapies that target synapse loss and circuit homeostasis. [ABSTRACT FROM AUTHOR]