The main component of the Center for Genetic Engineering and Biotechnology (CIGB)candidate vaccine against Hepatitis C virus (HCV)is the pIDKE2 plasmid. The current designed downstream process for the production of pIDKE2 fulfils all regulatory requirements and renders the required quantities of pharmaceutical-grade plasmid DNA (pDNA)with 95% purity. The advantages of this procedure include high plasmid purity and the elimination of undesirable additives,such as toxic organic extractants and animal-derived enzymes. However, yields and consequently the productivity of the process are low. Previous work demonstrated that the most criti-cal step of the process is the reverse phase chromatography,where conventional porous particle resins are used. Therefore,to increase the process productivity,alternative technologies such as membranes and chroma-tographic monoliths were tested as alternative options for this critical step. Here,a comparison between the behaviors of CIM?C4-HLD and Sartobind phenyl matrices was performed. To obtain higher productivities and purities,the dynamic binding capacities and selectivities were evaluated. The results showed that both matrices had a similar capacity for pIDKE2 plasmid,but the separation of pDNA isoforms using CIM technology was much better than that with Sartobind. Additionally,the optimal conditions for loading plasmid DNA on a CIM?C4-HLD 800-mL monolithic column in a real production process were determined. These optimizations will allow production levels to satisfy the high plasmid consumption demanded by clinical trials.