The biopharmaceutical market is one of the fastest growing biotechnology markets. In order to ensure affordable and reliable therapeutics, the biopharmaceutical process has to be closely monitored. Capillary electrophoresis (CE) has proven to be a valuable technique for the analysis of product concentration, critical quality attributes, product and process-related impurities, and nutrients and metabolites in the cell culture medium. Capillary zone electrophoresis, capillary gel electrophoresis, and capillary isoelectric focusing are extensively used for product concentration, and size or charge heterogeneity determination. CE has a number of benefits for the analysis of upstream and downstream process-intermediates, including the ability to handle highly complex matrices found in process-intermediates, high resolving power, little sample preparation requirements, rapid analysis, and low solvent and sample consumption. The small sample volumes (nL range) are especially beneficial for microbioreactor analysis or clone se-lection experiments. The simple setup and the possibility for miniaturisation and automation using microchip CE provides great opportunities for on-site, real-time monitoring of the process. This review discusses CE applications in upstream and downstream processing of the last decade.