Pharmacophore-based virtual screening is an effective, inexpensive and fast approach to discovering useful starting points for drug discovery.In this study, we developed a pharmacophore model for the main proteinase of severe acute respiratory syndrome coronavirus (SARSCoV).Then we used this pharmacophore model to search NCI 3D database including 250, 251 compounds and identified 30 existing drugscontaining the pharmacophore query. Among them are six compounds that already exhibited anti-SARS-CoV activity experimentally. Thismeans that our pharmacophore model can lead to the discovery of potent anti-SARS-CoV inhibitors or promising lead compounds for furtherSARS-CoV main proteinase inhibitor development.