Fractionation of flax shives into cellulose, hemicellulose, and lignin with a two-stage extraction process using water and aqueous ammonia was carried out in a pressurized low-polarity water extractor operated at different temperatures, flow rates, and ammonia concentrations. During the first stage with water, 84% of hemicellulose and 32% of lignin were removed at 190 degrees C at a flow rate of 1.5 mUmin for 30 min. During the second stage with aqueous ammonia, more than 77% of the lignin was removed, and hemicellulose removal reached 95% at 200 degrees C at a flow rate of 0.5 mUmin and with a solvent/feed ratio of 40 mL/g. The temperature and flow rate had a significant effect on lignin removal. The impact of additives (anthraquinone and hydrogen peroxide) and modifications (overnight soaking, reduced particle size, and elevated temperature) on lignin extraction was also studied. The combination of higher temperatures and reduced particle sizes resulted in enhanced lignin extraction. The extraction profiles of free phenolics (vanillin, acetovanillone, and vanillic acid) during the two-stage processing were monitored and compared with those of lignin.