The object of the study was fungous diseases occurring on roots, leave sheaths and stem base of winter wheat in the two opposing cropping systems (organic and conventional). The observations were made in vegetation periods (2007-2009) in the fields of winter wheat in northern Poland. Every year on each plot of compared farming systems root rot occurred (Fusarium spp., Gaeumannomyces graminis and other fungi). For the period of 3 years the degree of disease injury on the roots of winter wheat grown in the conventional system in the vegetation period increased, while in the organic one remained on pretty the same level. On average a lot more affected roots, especially in the flowering stage, occurred on the winter wheat grown in the conventional system. Fusarium foot rot (Fusarium spp.) developed on the wheat during the entire vegetation period. It was the most dangerous root and foot rot disease (the highest indexes of injury). The mean degree of disease injury on leave sheath was on pretty the same level in the two farming systems, although in investigated vegetation periods differed a lot, whereas at the bases of stems the pathogen was on the higher level on the wheat in the conventional system. Also eyespot (Tapesia yallude) developed in the entire vegetation period of the winter wheat, but its intensity was much lower than in case of fusarium foot rot. Leave sheaths of the wheat grown in the conventional system were slightly stronger affected than those grown in the organic system. In the flowering stage the intensity of the disease in both farming systems became equal, while in the wax maturity it was considerably higher in the conventional system. Sharp eyespot (Rhizoctonia spp.) appeared relatively late and occurred only in two years of investigation. The intensiveness of the disease was definitely higher on the organic plots. Among the affected roots, taken in the stem elongation stage, from the organic system 28 cultures of fungi were isolated, and from the conventional one 24 colonies. Cereals pathogenic fungi amounted 35.8% of isolates obtained from the organic system and as many as 66.7% from the conventional system. Among the affected roots, taken in the flowering stage, from the organic system 68 cultures of fungi were isolated in all, and from the conventional one 25 colonies. Cereals pathogenic fungi amounted 38.2% of isolates obtained from the organic system and 56.0% from the conventional system. Among the affected stem bases, taken in the wax maturity stage, from the organic system 56 cultures of fungi were isolated in all, and from the conventional one 52 colonies. Cereals pathogenic fungi amounted 48.4% of isolates obtained from the organic system and 53.6% from the conventional system. In the case of all root and foot rot diseases of wheat grown in the organic system, an advantageous influence of greater biodiversity and number of various fungi species living in root proximity was noticed as opposed to the conventional system.