The effects of genetic and environmental factors on the content and composition of steryl ferulates in wheat and rye were studied. The wheat and rye genotypes were grown at the same location in Hungary over three consecutive years (28 genotypes) or at four different locations across Europe during a single year (12 genotypes). The steryl ferulates were analyzed using HPLC. The genotype and growing location significantly affected the content and composition of wheat steryl ferulates, whereas the year of growth did not result in considerable variation. Less variation was observed in rye, due to fewer genotypes. Campestanyl and sitostanyl ferulates were the main species in both cereals. Knowledge of the natural variation in steryl ferulates and other bioactive compounds allows cultivators and plant breeders to select genotypes with high, stable levels of beneficial compounds. Thus, it is possible to enhance the intake of health-promoting compounds from natural sources.