A new cysteine sulfoxide containing a pyridyl residue was identified in bulbs of Allium L. species belonging to the subgenus Melanocrommyum section Megaloprason. One of these species, Allium stipitatum, is widely used as a crop plant and in folk medicine in Central Asia. The new cysteine sulfoxide was identified as L-(+)-S-(2-pyridyl)-cysteine sulfoxide. Aside from this cysteine sulfoxide, several pyridyl compounds could be identified, which were formed out of cysteine sulfoxides by the action of alliinase. Found cysteine sulfoxides and their metabolites are chemically unstable; thus, the analysis is rather difficult. By combining high-performance liquid chromatography (HPLC), HPLC tandem mass spectrometry, NMR, IR, and photometric methods, full structure elucidation of the cysteine sulfoxide was possible. Alliinase reaction products were mainly determined by various MS techniques. The achieved results give new insights in the chemistry of Allium crop plants and are probably useful for chemotaxonomical classification of the subgenus Melanocrommyum.