Deoxynivalenol (DON) is a mycotoxin produced by several Fusarium species and is toxic to a wide range of organisms, including human beings and livestock. To produce large amounts of pure DON for research purposes, a novel method using high-speed counter-current chromatography (HSCCC) was developed. Rice cultured with Fusarium graminearum and field mouldy corn infected by F. graminearum were extracted with methanol and found to contain 1.16 and 1.30 mg DON/g, respectively. The extracts were concentrated and then separated using a biphasic solvent system consisting of ethyl acetate-water (1:1, v/v). Collected fractions were analyzed by high-performance liquid chromatography (HPLC) and identified by congruent retention time and UV/vis spectrum and mass spectrometric data. Fractions containing DON were combined and freeze-dried. This method produced 116 mg and 65 mg DON with a purity of greater than 94.9% from 200 g of the rice culture and the mouldy corn, respectively. The HSCCC method had a recovery rate of DON at 88% from the crude extracts of both samples. This one-step purification method provided a simple and effective tool for obtaining a large amount of DON, an essential material for studies related to toxicology and detoxification of this mycotoxin.