The selective oxidation of methyl p-tolyl sulfide (MTS) to the corresponding sulfoxide (MTSO) by peroxyacetic acid and the subsequent rapid separation of the sulfide and sulfoxide are the basis for a fast and reliable HPLC method for the determination of this oxidizing agent in the presence of hydrogen peroxide. The time required for chromatographic separation was reduced to less than 1 min. To improve the long-term stability of the sulfoxide solution, hydrogen peroxide was decomposed catalytically by manganese dioxide. Even in the presence of a tenfold molar excess of hydrogen peroxide, a storability of at least 20 h without a significant increase in MTSO concentration was achieved. External calibration can be performed using the stable and commercially available MTSO. Real samples from a brewery cleaning-in-place disinfection process were analysed and the results were compared with those of the classical two-step titration.