Fatty acid steryl esters (FASE) in whole meal of 14 genotypes of tetraploid wheats (Triticum dicocconand T. durum) and 17 genotypes of hexaploid wheats (T. spelta and T. aestivum) were analyzed using different chromatographic strategies. By both GC-FID and HPLC-ELSD, tetraploid wheats are lacking two major peaks. The amounts of FASE, calculated on the basis of the GC-FID analysis, were double in hexaploid species as compared to tetraploids (40 and 20 mg/100 g db, respectively). HPLC with ESI-MS detection enabled the identification of FASE by the characteristic fragmentations and ion-adducts of each molecule. The distribution of steryl residues was not different between the wheat species: the main class of steryl derivatives found was the beta-sitosteryl derivatives, followed by campesteryl derivatives with small amounts of stigmasteryl esters. The esterified fatty acids explain the difference between the hexaploid and tetraploid wheats. In particular, small amounts of campesteryl and beta-sitosteryl, while no trace of stigmasteryl palmitates, were found in T. durum or its hulled ancestor T. dicoccon. Steryl oleates were not detectable in T. aestivum or its hulled ancestor T. spelta, which is consistent with the filogenesis of tetraploid and hexaploid species. Both chromatographic techniques (GC and HPLC) showed that FASE are useful to discriminate between hexaploid and tetraploid wheats from both qualitative and quantitative points of view.