A method for the simultaneous quantitation of total glutathione and total cysteine in wheat flour by a stable isotope dilution assay using high-performance liquid chromatography/tandem mass spectrometry (HPLC-MS/MS) was developed. As internal standards, L-[(13)C3, (15)N]cysteine and L-gamma-glutamyl-L-[(13)C3, (15)N]cysteinyl-glycine were used. The method consisted of the extraction and reduction of flour with tris(2-carboxyethyl) phosphine after the addition of internal standards, protection of free thiol groups with iodoacetic acid, derivatization of free amino groups with dansyl chloride, and HPLC-MS/MS. The limits of detection and quantitation for glutathione were 0.75 nmol/g and 2.23 nmol/g flour, respectively. For cysteine, the limits of detection and quantitation were 0.72 nmol/g and 2.12 nmol/g flour, respectively. The developed method was found to be sensitive enough for quantitation of total glutathione and cysteine levels in wheat flour. This method was then utilized to investigate the effect of sulfur (S) deficiency on the amount of total glutathione and cysteine in flour. In S-deficient wheat, the concentrations of total glutathione and cysteine were proportional to the amount of S supplied during growth. The calculation of correlations revealed that GSH and Cys concentrations influenced the rheological dough properties and the baking performance at least as much as protein parameters. Thus, the low concentration of GSH and Cys in flour from S-deficient wheat had a similar effect on the technological properties as the altered composition of gluten proteins.