The production of fatty acid methyl ester (FAME) by direct in situ alkaline-catalyzed transesterification of the triglycerides (TG) in cottonseeds was examined. The experimental results showed that the amount of cottonseed oil dissolved in methanol was approximately 99% of the total oil and the conversion of this oil could achieve 98% under the following conditions: less than 2% moisture content in cottonseed flours, 0.3-0.335 mm particle size, 0.1 mol/L NaOH concentration in methanol, 135:1 methanol/oil mole ratio, 40 degrees C reaction temperature and 3 h reaction time. Further, the effects of co-solvent petroleum ether and methanol recycling on the cottonseed oil extraction and conversion were also investigated. The use of alkaline methanol as extraction and reaction solvent, which would be useful for extraction oil and gossypol, would reduce the gossypol content in the cottonseed meal. The free and total gossypol contents in the cottonseed meal obtained from in situ alkaline transesterification were far below the FAO standard. And the nontoxic cottonseed meal could be used as animal protein feed resources. Crown Copyright (C) 2008 Published by Elsevier Ltd. All rights reserved.