The downstream purification steps comprise the most important part of the manufacturing of therapeutic proteins. The upstream process accumulates a large number of impurities including viruses, electrolytes, and other uncharged degradation products and structurally related molecules. Cleaning out these unwanted components to a level where it can comply with compendial requirements where available is accomplished in the purification steps. The chromatography techniques used can add contaminants of their own, causing protein degradation or modification of protein structure. Additionally, the yield obtained through the purification process is critical in making the system commercially feasible. Establishing optimal separation on a cost-effective basis requires a good understanding of the physicochemical nature of the target protein, particularly its physical and chemical stability profile. The first part of this chapter deals with the properties of protein that can have a significant effect on its separation potential; this is followed by a description of the most commonly used chromatography techniques.