In this paper the issues and challenges presented 15 years ago for performing efficient separation processes for recombinant proteins are revised and discussed. Competitive advantage in production was seen as not only dependent on innovations in molecular biology and other areas of basic biological sciences but also on innovation of separations and downstream processes. The trend to develop techniques that exploit fundamental physicochemical principles more efficiently was emphasized, including analysis of the physicochemical properties of proteins and its relation to efficiency in bioseparation. 15 years ago the main thrust was also focused on the development of novel techniques. Clearly the challenges faced today, where highly optimized and efficient production processes exist, are dramatically different. The use of mathematical models for optimizing chromatographic separations and simplifying validation of such operations is extremely advantageous. Their use constitutes an example of how the challenges that bioseparations are facing and will be facing within the next few years can be met. Such models should be extended to a larger number of proteins, chromatographic procedures and experimental conditions. (c) 2008 Society of Chemical Industry.