Ethanol was produced at pilot scale from rice straw hydrolysates using a Pichia stipitis strain previously adapted to NaOH-neutralized hydrolysates. The highest ethanol yield was 0.44 +/- 0.02 g(p)/g(s) at an aeration rate of 0.05 vvm using overliming-detoxified hydrolysates. The yield with hydrolysates conditioned by ammonia and NaOH was 0.39 +/- 0.01 and 0.34 +/- 0.01 g(p)/g(s), respectively, were achieved at the same aeration rate. The actual ethanol yield from hydrolysate fermentation with ammonia neutralization was similar to that with overliming hydrolysate after taking into account the xylose loss resulting from these conditioning processes. Moreover, the ethanol yield from ammonia-neutralized hydrolysates could be further enhanced by increasing the initial cell density by two-fold or reducing the combined concentration of furfural and 5-hydroxymethyl furfural to 0.6 g/L by reducing the severity of operational conditions in pretreatment. This study demonstrated the potential for commercial ethanol production from rice straw via xylose fermentation. (C) 2012 Elsevier Ltd. All rights reserved.