This chapter describes the procedures for production of recombinant hepatitis C virus (HCV) NS3 protease from clinical samples, which can be used in the biochemical assays to assess the impact of different drug-resistant mutations in the NS3 protein from patients under therapy of protease inhibitors. It gives the details of expression and purification of NS3 protease using the pCold vectors that contains a promoter derived from the cold-shock genes to drive the expression of NS3 protein. This robust protocol enables a medium-throughput production of HCV NS3 proteins of all genotypes and sequences derived from patient specimen.