Some components, primarily proteins, from cereal grains can trigger a number of clinical symptoms which can affect health and quality of life. The α-amylase trypsin inhibitors (ATIs) present in the cereal grains are believed to be elicitors for non-coeliac gluten sensitivity (NCGS) in some individuals, but the composition and abundance of ATIs in major cereal cultivars such as wheat and barley are not available. Here, discovery proteomics data revealed the presence of 24 and 21 ATIs from wheat cultivars Chara and Magenta, respectively; whilst 12 and 14 ATIs, respectively detected from barley cultivars Hindmarsh and Commander. Next, a recently developed two-step ATI-specific extraction protocol followed by targeted LC-MRM-MS-based experiment was employed to monitor the ATI quantities across 15 commercial wheat cultivars, the 8 parental lines from a multi-parent advanced generation intercross (MAGIC) wheat population and 12 commercial barley cultivars. The results showed that the dimeric (0.19+0.53) and CM3 ATIs comprised ~45% of the total measured ATIs, whilst monomeric (0.28) ATIs comprised 14%, CM1 (7%), CM2 (14%), CM16 (14%) and CMx comprised (7%) within wheat and MAGIC cultivars. Notably, the measured ATI content was decreased (~50%) in the wheat cultivars Janz, Sunvale, Diamond Bird and Longreach Scout. Compared to the MAGIC parent lines the ATI content was decreased by ~40% in a reference wheat cultivar Chara. In barley, the ATI peptide level variation (biological) ranged between 5-35% across the 12 commercial lines. The barley cultivars Oxford and Yagan contain higher levels (~135% relative to the average barley ATI content), whereas cultivars Fleet and Bomi contained the lowest levels (~61% and 80% respectively). This approach employing detection and relative quantitation of ATIs would be applicable to identify or develop wheat/barley cultivars with a significantly lowered level of ATIs that might be suitable for people with NCGS.