In this study, we assessed the efficacy of the specific knockdown of matrix metalloprotein-9 (MMP-9) in vitro and in vivo using short hairpin RNA (shRNA) against MMP-9. Two plasmids were generated encoding shRNA (pshRNA) targeted against two distinct MMP-9 gene sequences. Transfection of these pshMMP-9s could be shown to specifically inhibit MMP-9 expression both in vivo and in vitro. The effect occurred in vitro both in cells that endogenously produce MMP-9 and in cells exogenously transfected with an MMP-9-encoding plasmid. Using an in vivo transfection approach, the pshMMP- 9 was also effective at inhibiting MMP-9 protein expression in the mouse cornea. pshMMP-9s were also tested against herpes simplex virus (HSV) in the cornea. Delivery of the pshMMP-9 stopped angiogenesis and decreased the severity of herpetic keratitis. However, interferon-alpha (IFN-alpha) and IFN- beta induced by pshRNA might also contribute to inhibition of herpetic simplex keratitis (HSK) in the cornea.