The resurgence of the research of biomass processing is demanding novel methods facilitating the monitoring of lignocellulose processing. Here we demonstrate the suitability of capillary electrophoresis (CE) in the analysis of hydrothermal pre-treatment and enzymatic hydrolysis of pre-treated willow. CE enabled simultaneous separation of different saccharides and pre-treatment by-products of lignocellulose, furfural and 5-hydroxymethylfurfural. The excellent agreement between the results from CE and HPLC was established. CE was also found to be suitable for the monitoring of cellulose degradation in ionic liquid, 1-butyl-3-methylimidazolium chloride. (C) 2012 Elsevier B. V. All rights reserved.