A key barrier to the commercialization of fuels and chemicals produced from lignocellulosic biomass is the high cost and relative inefficiency of converting biomass into fermentable sugars. Dilute acid pretreatment is a promising technology for increasing the enzymatic digestibility of lignocellulosic biomass. A better understanding of the pretreatability of biomass is needed so that the rate and yields of sugars can be increased. Corn stover has been identified as a good feedstock for conversion into sugars and ethanol, however, different parts of the corn plant are physically, chemically and ultrastructurally distinct from one another, and so can be expected to respond differently to dilute acid pretreatment and enzymatic saccharification reaction conditions. We have characterized the changes in plant cell wall chemistry that occurred in selected anatomical fractions of corn stover during pretreatment over a range of severities. The fractions include nodes, internode stems, leaves, cobs and sheaths. The release of sugars from dilute acid pretreatment of corn stover anatomical fractions will be described and related to the gross chemical composition of the fractions. Ethanol yields from simultaneous saccharification and fermentation of selected samples will also be reported. Impacts on the yields of sugars from whole corn stover will be discussed and causes for the differences in behavior of the fractions considered.