Matrix metalloproteinase-9 (MMP-9, Gelatinase B), an extracellular-acting Zn2+-dependent endopeptidase, are involved in brain pathologies including ischemia, glioma, and epilepsy. Recent studies suggested that MMP-9 plays an important role in neuronal plasticity, specifically in learning and memory. To determine whether and how MMP-9 plays role in alcohol-related behaviors, male Sprague–Dawley (SD) rats were subjected to chronic intermittent ethanol (CIE) exposure for 4 weeks, following which we collected tissue samples from the hippocampus, medial prefrontal cortex (mPFC), and amygdala at different stages (acute and chronic exposure) during alcohol exposure. Real-time PCR and western blot assays were used to detect changes in the mRNA and protein expression of MMP-9. Our results indicated that both acute and chronic alcohol exposure induced up-regulation of MMP-9 mRNA levels in the hippocampus and mPFC, but not in the amygdala. Furthermore, acute and chronic alcohol exposure up regulated the expression of total MMP-9 and active MMP-9 in these two brain regions. Moreover, the increase of active MMP-9 expression was larger than those in total MMP-9 expression. Immunoprecipitation analyses identified potential MMP-9-interacting proteins, including Itgb1, Src, Eef1a2, tubulin, actin, and histone H2B. These results demonstrate that both acute and CIE exposure induced increases in MMP-9 expression in the mPFC and hippocampus, suggesting that MMP-9 plays a key role in chronic alcohol exposure and dependence. [ABSTRACT FROM AUTHOR]