One of the characteristics of ongoing demyelination in multiple sclerosis (MS) is the accumulation of lipid-laden macrophages in active lesions. Little is known about the source of these macrophages in the early stages of plaque evolution as microglial-derived and haematogenous macrophages share morphological characteristics and most cell surface antigens. A key issue in understanding the pathogenesis of MS is the reliable identification of phagocytes capable of degrading myelin and presenting autoantigen to T cells at the onset of demyelination. Using a combination of histochemistry and immunocytochemistry, an average of 60% of EBM11+ phagocytes (EMBII is a pan-macrophage marker) in early active MS plaques, defined as lesions with myelin-containing phagocytes but no obvious parenchymal myelin loss around these cells, were judged to originate from microglia as they exhibited nucleoside diphosphatase activity, a microglial marker. Only 4-15% of EBM11+ phagocytes in these lesions exhibited non-specific esterase activity, an enzyme marker for monocytes and macrophages. In contrast, 30-80% of EBM11+ phagocytes in more advanced active plaques with partial or complete myelin loss in the parenchyma were non-specific esterase+. Lysosomal enzyme acid phosphatase activity was strongly exhibited by 90% of phagocytes in all active plaques and there was a significant correlation between numbers of acid phosphatase+ cells and oil red O+ foamy macrophages. The results indicate that microglia are the main population of phagocytes in the early stages of demyelination and may play an important role in the pathogenesis of MS.