We used a modified pial vessel disruption (PVD) protocol with adult male Wistar rats to mimic small-vessel stroke in the cerebral cortex. Within 3 weeks, this lesion develops into a single lacuna-like cavity, which is fluid-filled and encapsulated by reactive astrocytes. Minocycline treatment that commences 1 hr after lesion and continues for 6 days prevents the cavitation and causes a filling of the lesion with reactive astrocytes and no barrier. Here, we determined whether inhibition of matrix metalloproteinases-2 and -9 (MMPs) mediates this minocycline action. Confocal microscopy revealed increased punctate staining of MMPs inside the lesion sites after 2 days of PVD. Astrocytes lined the lesion border but showed sparse localization inside the lesion. In contrast, increased MMP levels inside the lesion coincided with increased ED1 or OX-42 immunostaining, suggesting that MMP elevation reflected increased secretions from microglia/macrophages. Imaging analyses also revealed that minocycline administered for 2 days before animal euthanasia, significantly decreased MMP levels within the lesion. Moreover, Western blot analysis of cortical tissue extracts showed a significant 30–40% upregulation of MMPs 2 days after lesion. Minocycline administered 2 hr before the lesion significantly inhibited both MMP-9 and MMP-2 levels by ˜40%. In contrast, minocycline administered 1 hr after the lesion only decreased MMP-9 levels by ˜30%. Because MMP inhibition with batimastat injection also prevented cavity formation at 21 days, we conclude that minocycline prevented the creation of a lacuna-like cyst in the cerebral cortex by inhibiting the MMP secretion from microglia in the affected tissue. © 2013 Wiley Periodicals, Inc.