Various Allium hybrids, obtained by the crossbreeding of Allium cepa (onion) as the mother plant and six taxonomically distant wild species obtained by embryo rescue, were investigated with special respect to their individual profiles of cysteine sulfoxides as well as enzymically and nonenzymically formed aroma substances. Alliinase (EC 4.4.1.4) catalyzes the conversion of odorless (+)-S-alk(en)yl-L-cysteine sulfoxides into volatile thiosulfinates. These thiosulfinates were converted to a variety of sulfides by steam distillation. SPME-gas chromatography (GC) and high-performance liquid chromatography (HPLC) used for the analysis of aroma components and their precursors permitted a high sample throughput, so that numerous gene bank accessions and Allium breeding materials were analyzed within a comparatively short time. Cysteine sulfoxides as well as alliinase activity were found in all investigated samples at different levels, but (+)-S-methyl-L-cysteine sulfoxide (methiin) was the most abundant sulfoxide present. (+)-S-(trans-1-Propenyl)-L-cysteine sulfoxide (isoalliin) is typical for onion and was found in all investigated hybrids. The pattern of the other cysteine sulfoxides depended strongly on the parent plants used. The profile of aroma components corresponded with the related pattern of aroma precursors (cysteine sulfoxides). Successful hybridization was proven by randomly amplified polymorphic DNA analysis. Together with these established marker techniques, HPLC and SPME-GC analysis provide support to breeding projects designed to improve the health and aroma properties of Allium hybrids.