Hydrothermal pretreatment of lignocellulosic biomass is a cost effective technology for second generation biorefineries. The process occurs in large horizontal and pressurized thermal reactors where the biomatrix is opened under the action of steam pressure and temperature to expose cellulose for the enzymatic hydrolysis process. Several by-products are also formed, which disturb and act as inhibitors downstream. The objective of this study is to formulate and validate a large scale hydrothermal pretreatment dynamic model based on mass and energy balances, together with a complex conversion mechanism and kinetics. The study includes a comprehensive sensitivity and uncertainty analysis, with parameter estimation from real-data in the 178-185 degrees C range. To highlight the application utility of the model, a state estimator for biomass composition is developed. The predictions capture well the dynamic trends of the process, outlining the value of the model for simulation, control design, and optimization for full-scale applications. (c) 2015 American Institute of Chemical Engineers