This chapter deals with protein aggregation, which is a key issue in biopharmaceutical processes. Several experimental techniques to characterize the aggregate size and content are presented and fundamentals on the kinetic modelling of aggregation mechanisms are provided. The impact of operating conditions on the aggregation rate is reviewed and the steps critical for aggregate formation in biopharmaceutical processes are identified. Finally, methods aiming at reducing the aggregate content are proposed. These methods focus either on improving protein stability or on removing the formed aggregates. The former can be achieved by synthesizing aggregation-resistant proteins, tuning operating conditions, or designing processes with a shorter residence time (e.g. perfusion bioreactors or counter-current chromatography). The latter method is mainly achieved by filtration and chromatography. In particular, the simulated moving bed process is shown to be very advantageous for aggregate removal with size exclusion chromatography: it allows improving productivity, decreasing eluent consumption and increasing the outlet protein concentration as compared to single-column processes.