Traditional methods for evaluating sowing and technological characteristics of grain do not sufficiently reveal the caryopsis internal structure damages. They can only be recorded using the microfocus soft X-ray radiography method. The aim of this work was, with the help of X-ray, to evaluate the hidden integrity of the caryopsis structure (including the period of the post-harvest maturation) to increase the efficiency of expert assessment of the degree of economic suitability of grain batches. Seeds of Hordеum vulgare L. variety ‘Suzdalets’ harvested in 2015 in the Gatchina and Vsevolozhsk districts of the Leningrad region, malting barley from the Morskoy Port St. Petersburg (2015–2016), as well as corn grain (Zea mais L.) harvested in 2010 and 2011 were the objects of the research. Grain, which is for feed use only, was provided by the poultry farm “Severnaya”. The poultry farm “Roskar” provided samples harvested in 2017. We used the microfocus radiography method combined with a visual analysis of digital X-ray images to detect hidden grain defects. Experimental data on the evaluation of quality and biosafety of barley and maize grain for various purposes determined by radiographic signs of hidden damage are presented. The survey highlighted several key points: the seed lots obtained in the Vsevolozhsk district had a low total level of hidden defects (39 %); in the seed lots obtained in the Gatchina district, this figure was significantly higher (> 140 %). The germination rate for these options, determined six months after harvesting, turned out to be 89 and 74 %, respectively; it was higher for batches of seeds with a small value of the total indicator of hidden defects. Samples, the total level of hidden defects of which was lower (29 %), had a higher germination index (97 %) compared to the same in seed samples with a total level of hidden defects 70 % or more (85–90 %). X-ray analysis of corn grain samples obtained at the poultry farm “Roskar” revealed that the amount of grain with defects in the embryo (hidden germination) compared with the same in grain lots from the poultry farm “Severnaya” was low and varied from 17 to 29 %. The index of the hidden fissuring rate in these samples was not reliably recorded. However, we detected such internal grain damage as enzyme mycosis depletion (64 to 98 %). Research results are the basis for the development of new engineering and technical solutions for the “gentle” agricultural technologies to obtain batches of high-quality non-injured grain that ensure high competitiveness in the global grain market.