The biotechnology industry has undergone rapid growth in recent years largely due to the development and success of protein-based therapeutics for a wide range of disorders. Similar to traditional pharmaceuticals, characterization of a therapeutic protein for its physicochemical properties, process monitoring and lot release is crucial. Electrophoresis in the slab-gel format has and continues to be a mainstay of the protein laboratory; and more recently, CE has begun to make significant inroads for protein analysis in industrial settings. This review focuses on the electrophoresis of proteins with an emphasis on protein-based therapeutics in the capillary, slab-gel and to a lesser extent, the microchip format. Reported applications of electrophoresis at several stages of the biopharmaceutical industry covering the period of 2000-2005 will be discussed.