The efficiency of biomass utilization can be significantly improved by fractionation of biomass. A two-stage percolation process was investigated for pretreatment and fractionation of corn stover. The two-stage process is composed of hot water treatment followed by treatment with aqueous ammonia, both applied in a flow-through (percolation) reactor. The first stage processing is intended for hemicellulose removal whereas the second stage is intended for delignification. The pretreated material was nearly pure cellulose and both reagents are cheap and environmentally friendly. The conditions that achieve satisfactory level of biomass fractionation and acceptable enzymatic hydrolysis were identified in terms of reaction temperature, flow rate (retention time) and reaction time for each stage. With proper operation of two-stage treatment, fractionation of biomass was achieved to the extent that the xylan fraction is hydrolyzed with 92-95% conversion, and recovered with 83-86% yields; and the lignin removal is 75-81%. The remaining solid after two-stage treatment contained 78-85% cellulose. The two-stage treatments enhanced the enzymatic digestibility to 90-96% with 60 FPU/g of glucan, and 87-89% with 15 FPU/g of glucan. In two-stage treatment, the composition and digestibility data indicate that the lignin content in the biomass is one of the major factors controlling the enzymatic digestibility. (c) 2005 Published by Elsevier Ltd.