Malt is one of the most important contributors to beer flavor, this research aimed to characterize the volatile profiles of two varieties of pigmented corn in their unmalted and malted form and determine the differences and similarities between pigmented corn malts and barley malts. A total of 173 volatiles were identified, where phenols and terpenes such as 2-meyhoxy-4-vinylphenol, phenol, 4-ethyl-phenol, limonene, and geranyl acetone are the main compounds that characterize pigmented corn malts. Volatiles such as 4-ethyl-phenol,4-ethyl-2-methoxy-phenol, limonene, geranyl acetone, and α-terpineol might be considered as flavor markers of the red and blue corn grains and corn malts. The results demonstrated there is a group of volatiles specific to corn malts and others that have in common to barley malt. These volatiles can be used as specific key markers for pigmented corn malts. The similarities between barley and corn malts open the possibility to use pigmented corn for brewing purposes. Practical applications The similarities between corn and barley malts in their volatile profiles make pigmented corn a good alternative to produce beers using native ingredients from Mexico.