The objective of the study was to compare health status of harvested grain of spring barley cv. Rudzik, Rodos, Start and Maresi cultivated in organic system and cv. Damazy grown in an organic farm. Analyses showed that prevalent pathogen on grain was <i>Bipolaris sorokiniana</i> isolated from 48% of grains. Fungi from genus of <i>Fusarium</i> were obtained less numerously, from 27% of grains and were represented mainly by <i>F. poae</i> and <i>F. avenaceum</i>. Microscopic analysis of <i>F. poae</i> was confirmed by PCR analysis. All cultivars were intensively diseased by <i>B. sorokiniana</i>, thus it is impossible to show a cultivar especially recommended for this system, where <i>B. sorokiniana</i> can be serious problem. However cv. Damazy showed relatively the lowest infestation by <i>B. sorokiniana</i> and it also was not more intensively diseased by <i>Fusarium</i> spp. It is very important in nutrition aspect because these fungi can be dangerous for both human and animal health due to their abilities to produce mycotoxins.