The goal of biomass pretreatment is to increase the enzymatic digestibility of the plant cell wall polysaccharides to produce sugars for upgrading to biofuels. Alkaline pretreatment has the ability to solubilize much of the lignin in biomass while the carbohydrates remain insoluble. With an increased research focus to produce high-value products from lignin, a low molecular weight, lignin-rich stream in a biorefinery is desirable. Here, this work reports on batch alkaline pretreatment of corn stover conducted using a three-factor, two-level central composite experimental design in a pilot-scale reactor to determine the relationship between sodium hydroxide (NaOH) loading, temperature, and anthraquinone (AQ) charge on solids solubilization, component yields, and enzymatic digestibility of the residual solids. Operating conditions were 100 to 140 �C, 40 to 70 mg NaOH/g dry corn stover, and 0.05% to 0.2% (w/w) AQ loading. An enzymatic hydrolysis screening study was performed at 2% cellulose loading. Empirical modeling results showed that NaOH loading and temperature are both significant factors, solubilizing 15% to 35% of the solids and up to 54% of the lignin. Enzymatic hydrolysis of the residual solids produced good monomeric glucose (>
90%) and xylose (>
70%) yields at the more severe pretreatment conditions. We also found that the AQ charge was not a significant factor at the conditions studied, so efforts to reduce xylan and increase lignin solubilization using this compound were not successful. Lastly, while good lignin solubilization was achieved, effectively recovering this stream remains a challenge, and demonstrating performance in continuous reactors is still needed.