Natural fermentation was tested as a method of releasing active compounds during screening for potential anticoagulant activity in three types of algae (Pachymeniopsis elliptica, Sargassum horneri, and Ulva pertusa). Freeze dried algae samples (2.5 g) were fermented by adding 75 g of sugar and 500 mL of water and thereafter kept at room temperature (25 degrees C) for 3 months. Activated partial thromboplastin time (APTT), prothrombin time (PT), and thrombin time (TT) were measured every 2 weeks for 3 months to determine the optimum time for the highest activity. Fermented P. elliptica, (which had the highest activity) was subjected to anion exchange chromatography (DEAE-cellulose) and sepharose 4B gel permeation chromatography. The purified sample was analyzed by agarose-gel electrophoresis and polyacrylamide gel electrophoresis (PAGE) to confirm the purification and to determine the molecular mass, respectively. The 360 mu g/mL of purified compound (Mwt > 500,000 Da) had both APTT and PT activities (> 1,000 s). However, at the concentrations of 180 mu g/mL, purified compound and heparin showed 540 and > 1,000 s APTT activity, respectively. Though, the purified compound of P. elliptica considered as a weaker anticoagulant than heparin, this purified anticoagulant polysaccharide could be considered as a good alternative source as an anticoagulant. Moreover, the technique of fermentation is an inexpensive and feasible, this purified anticoagulant polysaccharide compound could be used in pharmaceutical and biomedical industry. Further investigations need to be performed to determine the mechanism of this novel anticoagulant compound.