The immediate challenge in the fractionation and purification of biofunctional oligosaccharides, for example enzymatically manufactured prebiotics, is the coupling of chemical engineering knowledge on mass transport and membrane separation to the particular requirements and opportunities provided by carbohydrate-based products. This review provides an overview of the currently available knowledge and correlations between the particular properties of saccharides, e.g. their structural and physico-chemical characteristics, and membrane separation principles considering the potential influence of the operational modes and variables on the separation efficiency. The hitherto used membrane-based techniques, mainly ultra- and nanofiltration, and the conditions (membrane type, temperature, feed concentration, pressure) during separation and purification of different types of oligosaccharides are discussed. Lastly, the applicability of a number of novel separation techniques, vibrating membrane module, electrofiltration, and backflushing are presented in relation to high-performance separation of oligosaccharides. (C) 2009 Elsevier B.V. All rights reserved.