A field experiment was conducted in a randomized block design, in three replication, in Bałcyny (NE Poland) during the years 2008–2009. Rye cv. Dańkowskie Diament was grown under a conventional and organic crop rotation system. In the conventional system, rye plants were protected with the fungicide Juwel TT 483 SE, and an Effective Microorganisms (EM) bioproduct was applied in the organic crop rotation. In 2008–2009, the symptoms of Fusarium foot rot (Fusarium spp.) were noted most frequently on the stem bases of rye, while eyespot (Oculimacula spp.) was less common. The flag leaves were mostly infected by the pathogens Rhynchosporium secalis and Puccinia recondita f. sp. recondita. Disease severity was affected by weather conditions, which is why infection rates were substantially lower in 2008 than in 2009. In the organic system, in the second year of treatment with effective microorganisms, the rates of fungal infections of winter rye caused by the following pathogens: P. recondita f. sp. recondita and Oculimacula spp. were lower than in the conventional system.