The seeds of buckwheat (Fagopyrum esculentum Moench L.) were dehulled and then, following milling, extruded on a counter rotating, twin-screw extruder with the different barrel temperature profiles: 120, 160, and 200 degrees C. After extrusion cooking process, the following compounds were analyzed: free and conjugated phenolic acids, total polyphenols (TPC), tocopherols (T) and tocotrienols (T3), inositol phosphates (IP), reduced glutathione (GSH), and melatonin (MLT). The antioxidant capacity and superoxide dismutase-like activity (SOD-like activity) were determined in the groats and extrudates. Extrusion caused a significant decrease in all the compounds tested, except for phenolic acids. The content of IP decreased by 13%, that of GSH by 42%, and that of T + T3 by 62%. A three-fold lower level of MLT and TPC was noted whereas the SOD-like activity disappeared when compared to the nonextruded material. A two-fold higher content of phenolic acids (free and released from ester bonds) was observed. In spite of the clear decrease in the investigated antioxidants, the extruded dehulled buckwheat seeds contained still significant content of bioactive compounds, which resulted in as little as an average 10% decrease of the antioxidant capacity.