The loss of ethanol to waste (by-product) from distillation bottoms in bioethanol production plants can significantly affect the efficiency of fuel-grade ethanol production. Monitoring residual ethanol levels during distillation allows operators to adjust control parameters to minimize ethanol to waste and improve energy efficiency in plant operation. In this study ethanol was measured in both early and late stage distillation beer bottoms and side stripper bottoms, respectively, of a corn-based ethanol fermentation production process at a 40 MMGY bioethanol plant. The target operational value in both stages was 0.05% w/v ethanol. Samples of beer bottoms and side stripper bottoms were collected on thirty different days over a six week period. Each sample was measured with the YSI biochemistry analyzer and with an HPLC system. Comparability of the two analytical methods was evaluated with regards to precision and analysis time. A strong, positive correlation of the two methods was demonstrated. YSI analyzer results were obtained within 2 minutes after sample filtration, while HPLC results were available 35-40 minutes post-filtration. The YSI biochemistry analyzer provided rapid ethanol analysis allowing timely in-process data for improving plant efficiency and reducing operational cost.