Free sulfhydryl groups in sulfur compounds have been reported to act directly on natural toxins to reduce toxicity. The objective of this study was to reduce protease inhibitors and glycoalkaloids in simulated snack foods by the addition of sulfur-containing compounds prior to extrusion. Thiamine, methionine, and benzyl disulfide were added to potato flakes at levels of 0.5% or 1.0% prior to twin-screw extrusion. Total and free thiols and protease inhibitors were monitored before and after extrusion by colorimetric assays. Potato glycoalkaloids were analyzed by HPLC and by immunoassay. Extrusion reduced potato flake disulfide bonds; disulfide bonds were higher in samples containing added sulfur compounds. Trypsin inhibitor activity was reduced by as much as 79% by extrusion plus methionine. Extrusion significantly reduced carboxypeptidase inhibitor, but only when benzyl disulfide and 0.5% methionine were not added. One percent methionine and thiamine resulted in 60% reductions in glycoalkaloids.