The first critical challenge in the biomass conversion process is increasing the available surface area of the biomass for subsequent enzymatic hydrolysis with minimal formation of downstream inhibitory compounds. The implementation of a pretreatment methodology that can process a wide range of feedstocks with little variability in efficiency and yield is the most critical process step in the realization of an integrated lignocellulosic biorefinery. Biomass degradation products that result from some of these pretreatment methods typically include hydroxymethylfurfural (HMF) and furfural, which produce levulinic and formic acids that inhibit subsequent fermentation of sugars to ethanol. We are investigating the utilization of ionic liquids as a biomass pretreatment technology that may reduce the production of these inhibitory compounds and efficiently break down crystalline cellulose. We will present results that demonstrate how lignocellulosic material degrades in these ionic environments and correlate structural elements with compositional changes. A comparison of this technology with dilute acid pretreatment will also be presented.