Benzoxazinoids are important phytochemicals found in wheat and rye that are associated with plant resistance against pathogens, and recent studies have emphasized the potential health-promoting role of these compounds i.e. anti-cancer, anti-allergy and anti-inflammation. Accordingly, an understanding of their distribution in seeds and the effect of different processing techniques on their transformation will be helpful in identifying the mechanisms of their production and distribution and will support the on-going efforts to utilize these compounds in health-promoting food products. The analysis of seed fractions obtained from the milling of wheat and rye showed significantly higher concentrations of these bioactive compounds in the germ than in the other fractions, i.e. the bran and endosperm. Di-hexoses of 2,4-dihydroxy-1, 4-benzoxazin-3-one (DIBOA-glc-hexose) and 2-hydroxy-1, 4-benzoxazin-3-one (HBOA-glc-hexose) were the predominant compounds found in the different wheat and rye seed fractions followed by DIBOA-glc and DIBOA. The soaking and boiling of three rye-based breakfast cereals resulted in considerable changes in the benzoxazinoid contents. The soaking of pearled rye promoted the conversion of DIBOA-glc-hexose into DIBOA-glc. When these cereals were boiled, the increase in the DIBOA-glc content was much lower than that observed for soaking. For rye flakes, the pattern of these benzoxazinoids was different from that in pearled rye seeds. A considerable amount of the benzoxazinoids was also leached into the water during soaking or boiling. This study contributes to the understanding of the underlying processes involved in the biochemical changes of benzoxazinoids and will be the basis for future studies on other food-processing techniques.