Producing ethanol from cellulosic biomass has the potential to replace gasoline and benefit the environment by lowering net greenhouse gas (GHG) emissions. One option for producing ethanol from cellulosic biomass involves dilute acid pretreatment to solubilize the hemicellulose fraction into monomeric sugars (primarily xylose and arabinose). The solid residue left behind is rich in cellulose that can be enzymatically converted to monomeric glucose, which along with the hemicellulosic sugars can be fermented to ethanol. An accurate assessment of process performance requires precise measurement of the chemical composition of the pretreated biomass and process intermediates, particularly carbohydrate concentrations that are required to calculate pretreatment efficacy, degree of enzymatic digestion of the cellulose and ethanol yield. Typically, there are many compounds in these samples that make accurate measure of component concentrations very difficult. Often, a method that accurately measures one particular sugar is not appropriate for another sugar. We explored the efficacy of several instrumental methods for analysis of sugars and other compounds found in dilute acid pretreated corn stover solids after enzymatic hydrolysis and in the fermented hydrolyzate liquor. We compared results from the various methods and will discuss the pros and cons of each technique and make recommendations for further work.