β-Glucans from cereals are β(1-3)(1-4)-mixed linkage linear homopolysaccharides of d-glucopyranosyl residues, recently recognised as functional components of foods with benefits in maintaining the health of the digestive tract not least through a prebiotic effect. Here we describe the development of methodology to facilitate the study of β-glucans as prebiotics. Relatively short β-glucan fragments (DP 6-50) were produced by partial hydrolysis of β-glucan fibres with Lichenase then functionalised at their reducing end with a tetramethylrhodamine dye. Their enzymatic break down by human colon microbiota in an in vitro fermentation model was examined. Digestion products were isolated by virtue of their fluorescence labels, identified and characterised using capillary electrophoresis and mass spectrometry. Complete digestion of the labelled substrates was indicated, as fluorescently labelled glucose was obtained as the final product. Furthermore, a pathway of enzymatic breakdown was proposed on the basis of a time course experiment; initial fast hydrolysis with an endo-1,3(4)-β-glucanase was followed by slow degradation with an exo-1,4-β-glucanase and finally slow action of an exo-1,3-β-glucanase.