Deoxynivalenol (DON) is one of most widespread mycotoxins in cereal commodities, and animal feed is prevalently contaminated at high concentrations. This poses a problem in animal nutrition as especially pigs are very sensitive to DON. An effective process for the reduction of the DON concentration is the treatment of contaminated feed with sodium bisulfite (SBS) whereby DON is transformed into DON-sulfonate (DONS). Although the success of this treatment has been confirmed in several feeding studies, it is unexplained if the decrease of DON is accompanied with a coincident increase of DONS. For this reason, we developed a method for the analysis of DONS using hydrophilic interaction chromatography coupled to tandem mass spectrometry. In order to investigate the correlation between DON and DONS concentrations during SBS-treatment, DON-contaminated wheat was treated with SBS and stored for up to 36 days. At defined timepoints of this treatment, samples were analyzed for DON and DONS using stable isotope labeled standards. The preparation, purification, and structure elucidation of DONS, and the HILIC-HPLC-MS/MS method for the analysis of DONS as well as the results of two storage experiments are presented in this paper.