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Objective In focal cortical dysplasia type Ⅱb (FCDⅡb) and tuberous sclerosis complex (TSC), malformative cortical lesions in the cerebral cortex cause epilepsy and other neurological abnormalities.However, the mechanisms of epilepsy in FCDⅡb and TSC remains largely unkown.Recent evidences indicate that Matrix metalloproteinase 9 (MMP9) may be closely involved in epileptogenesis.In this study, we investigated whether MMP9 might be involved in malformations of cortical development (MCDs) associated with epilepsy.Methods We analyzed the expression and activity of MMP9 in FCDIIb lesions (n =9) and TSC tubers (n =13) and in control cortex (CTX, n =8) by immunoblotting.Immunohistochemical methods are used for the specific cellular distribution of MMP9.Results Elevation of protein levels and overactivity of MMP9 were observed in FCDⅡb and TSC lesions versus CTX.Immunohistochemical studies indicated that MMP9 was strongly characteristically expressed in misshappend cells, namely, hypertrophic neurons, dysmorphic neurons, balloon cells and gaint cells.Double immunofluorescent staining indicated that the reactive astrocytes, not the microglia, highly expressed MMP9.Conclusion These results suggest that overexpression and overactivity of MMP9 may contribute to the epileptogenesis of FCDIIb and TSC.