The morphology of microglia, which are immune cells in the brain, is strongly linked to their function. In particular, when phagocytosing dead cells or debris, the morphology of microglia is altered from their normal ramified structure. We have recently found that microglia with characteristic morphology cluster around hemorrhagic region in the brains of healthy newborn mice. The perinatal period is a critical period for brain development, and intracerebral hemorrhage during this period can cause irreversible brain damage. In particular, erythrocytes leaking into the brain parenchyma are cytotoxic and need to be removed rapidly. We found that erythrocytes are mainly phagocytosed by microglia. Pharmacological removal of microglia increased the number of leaking erythrocytes in the hemorrhagic region. Therefore, under physiological conditions, microglia may contribute to normal brain development by rapidly phagocytosing and removing leaking erythrocytes. Next, to examine the changes in microglial properties mediated by erythrophagocytosis, we performed a transcriptome analysis of erythrophagocytic microglia, finding that these microglia highly expressed several genes that are considered essential for erythrocyte processing. The expression of these genes may lead to the heterogeneity of microglia function in the mature brain.