Stem base health of spring barley cultivated under organic, integrated and conventional systems and fungal communities were studied. A worst plant health status was observed in the organic system. The macroscopic and subsequent mycological analyses revealed the occurrence of Bipolaris sorokiniana and Fusarium spp. The incidence of B. sorokiniana on stem bases was clearly dependent on a farming system, and the highest incidence of this pathogen was observed in the organic system. Also, in that system, Fusarium spp. were isolated more numerously in the beginning of tillering, but in dough stage B. sorokiniana was the most prevalent pathogen, and Fusarium spp. were more numerous in integrated and conventional systems. It is worth to note that organic conditions could be favourable to Gliocladium spp. Because of growing interest in ecology, excluding the use of pesticides and increasing popularity of biological disease control, these antagonistic fungi could be useful in organic systems.