Flowing hot water through cellulosic biomass offers many promising features for advanced pretreatment, and a better understanding of the mechanisms responsible for flowthrough behavior could allow us to capitalize on its key attributes while overcoming its limitations. In this study, extensive data were developed to show the effect of flow on the fate of hemicellulose, lignin, and total mass for hot-water pretreatment of corn stover in a small tubular flowthrough reactor at 180, 200, and 220 degreesC. Solubilization of hemicellulose increased with flow, especially at high temperatures; a result that is inconsistent with traditional first-order kinetic models. The dissolved xylan in the hydrolyzate was mostly oligomers over this temperature range, and the fraction as oligomers increased with flow rate. Also of importance, lignin removal increased from less than about 30% for batch reactors to about 75% at high flow rates and was nearly linearly related to hemicellulose release for the flowthrough reactor. These observations suggest that mass transfer or other physical factors, and not strictly first-order homogeneous chemical kinetics, impact hemicellulose hydrolysis. In addition, lignin appears to be released throughout hydrolysis, but its fate may be governed by subsequent precipitation reactions unless it is removed first.