We developed a purification method based on liquid chromatography-tandem mass spectrometry for the identification of deoxynivalenol (DON), its acetylated derivatives (3-acetyl-deoxynivalenol and 15-acetyl-deoxynivalenol), and a glycosylated derivative (deoxynivalenol-3-glucoside [D3G]) in corn-based products. The analytes were extracted from samples with acetonitrile-water (85:15, vol/vol) and then purified with multifunctional columns. Evaluation of five kinds of multifunctional columns revealed that DON and its acetylated derivatives were recovered well (96 to 120%) by all columns, but D3G was recovered adequately (93.5%) by only one column, InertSep VRA-3. Samples of corn grits and corn flour were analyzed using the purification method with InertSep VRA-3. DON, D3G, and 15-acetyl-deoxynivalenol were the major contaminants in the samples harvested in 2009, but only DON was detected in the samples harvested in 2010. These results suggest that the purification method using InertSep VRA-3 is effective for identification of DON and its derivatives in corn-based products.