Investigations concerned effect of organic and other farming systems on cereal health status. Research material were roots, stem bases, leaves, ears and harvested grain of winter wheat and spring barley. Results showed lower health of spring barley in organic system, while this farming system did not affect winter wheat negatively. Fusarium spp. were prevalent among pathogens of winter wheat in all systems and in the case of spring barley - in integrated and conventional system. The exception was organically grown barley where Bipolaris sorokiniana dominated. Alternative seed treatment methods used in these studies did not limit growth of B. sorokiniana considerably, but some tendencies to lower incidence of this species on barley seedlings were noted. Antagonistic strain of Trichoderma viride did not show advantageous effect as biological seed treatment agent