Severe acute respiratory syndrome associated coronavirus main protease (SARS-CoV M pro) has been proposed as a prime target for anti-SARS drug development. We have cloned and overexpressed the SARS-CoV M pro in Escherichia coli, and purified the recombinant M pro to homogeneity. The kinetic parameters of the recombinant SARS-CoV M pro were characterized by high performance liquid chromatography-based assay and continuous fluorescence-based assay. Two novel small molecule inhibitors of the SARS-CoV M pro were identified by high-throughput screening using an internally quenched fluorogenic substrate. The identified inhibitors have K i values at low μM range with comparable anti-SARS-CoV activity in cell-based assays.