The researched material was healthiness of roots and fungus composition of spring barley cultivated under organic, integrated and conventional farming systems. The studies were carried out in 1998-2001 on experimental fields in Osiny near Puławy, south-eastern Poland. In the emergence stage the roots health status was the lowest in organic system however in the end of vegetation season, in dough maturity stage the most disease symptoms were stated in conventional system. The mycological analyses revealed the occurrence of two important pathogens: <i>Bipolaris sorokiniana</i> and <i>Fusarium</i> spp. Despite of root healthiness macroscopic analyses showed their lower health status in organic system only in emergence stage and the most quantity of plants with disease symptoms in dough maturity stage were observed in conventional system, but pathogens like <i>Bipolaris sorokiniana</i> and <i>Fusarium</i> spp. were mostly isolated in organic system in both phases. It can suggest that disease symptoms in conventional system can be caused by different than fungus factors. The lowest percent of mentioned pathogens was stated in integrated system. It is worth to notice that organic conditions could be favourable to <i>Gliocladium roseum</i>. Because of growing interest in ecology, giving up of using pesticides and more and more popular biological disease control, these fungi of <i>Gliocladium</i> genus be used in this system due to their antagonistic properties.