Apoptosis of T lymphocytes is a common pathway to terminate autoimmune inflammation in the brain as shown in experimental autoimmune encephalomyelitis (EAE) and in the autoimmune inflamed human brain. To date it is unclear to what extent different glial cells are involved in the removal of apoptotic cells. In an in vitro phagocytosis assay we compared the phagocytic capacity of rat microglia cells to remove apoptotic lymphocytes with that of astrocytes. Apoptosis was induced in autologous thymocytes and myelin basic protein (MBP)-specific T-cells by methylprednisolone (MP) or by irradiation. Apoptotic cells were then added to glial cells that were untreated or prestimulated with interferon-γ (IFN-γ), interleukin-4 (IL-4), transforming growth factor-β (TGF-β), or tumor necrosis factor-α (TNF-α). Supernatants were collected from cell cultures to measure their cytokine secretion. Surface antigen expression was analyzed by flow cytometry. Both cell types significantly increased their phagocytic activity in response to the addition of apoptotic lymphocytes when compared to non-apoptotic cells (p < 0.0001). Astrocytes removed only up to one third of the number of apoptotic lymphocytes ingested by microglia cells (p < 0.0001). Microglia cells significantly increased their phagocytosis rate after IFN-γ stimulation and decreased it in response to IL-4. In contrast, astrocyte phagocytosis was almost unresponsive to cytokine stimulation. After interaction with apoptotic cells, microglia secreted significantly less TNF-α. Astrocytic TNF-α production was also decreased but not to a statistically significant extent. MHC-class II expression after phagocytosis was increased on microglia cells but not on astrocytes. Both microglia cells and astrocytes are capable of ingesting apoptotic cells, but microglia cells are much more efficient phagocytes. Their phagocytic capacity is modulated by the local microenvironment and microglial immune function is downregulated after phagocytosis. We suggest that in vivo astrocytes might be activated as phagocytes once the limit of microglial phagocytic capacity has been reached.