Benzoxazinoids are metabolites occurring in a restricted group of plant species including crops such as rye, wheat, and maize. Focus on the analysis of benzoxazinoid metabolites has typically been due to their importance to plant biochemistry and physiology as highly bioactive molecules that plants use as alleochemicals to defend themselves against predators and infections. However, the potential dietary contribution of these compounds has not been addressed. This study conducted a detailed qualitative characterization of benzoxazinoid metabolites present in the whole grain rye and processed fractions of rye bran, and their presence was also detected in whole grain wheat samples. Several novel benzoxazinoid metabolites of the hydroxamic acids (2,4-dihydroxy-1,4-benzoxazin-3-one, DIBOA; 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one, DIMBOA), lactams (2-hydroxy-1,4-benzoxazin-3-one, HBOA), and benzoxazolinones (1,3-benzoxazol-2-one, BOA) were identified, including double-hexose derivatives of DIBOA, DIMBOA, and HBOA. This paper presents an important addition to the information on the phytochemical composition of rye and wheat grains, which deserves attention in the discussion of the potential health-promoting effects of these grains.