Within the framework of long-term experiment devoted to cereal production, the factors variety and fungicide protection were added during three years (2006, 2008 and 2010) to the factors crop rotation and soil tillage already studied since 1967. This complement aimed at evaluating the influence of the cropping system on the development of diseases on winter wheat and discussing the impacts on yield. The favorable effect of sanitation measures such as crop rotation and ploughing was raised for eyespot, septoria leaf blotch and fusarium head blight. These preventive measures could be reversed by environmental conditions favorable to the later disease development. Powdery mildew and brown rust were further influenced by the environmental conditions favorable to their development. The concentration in fusarium mycotoxins depended more on the presence of previous maize than on winter wheat in monoculture. The importance of the ploughing or a tolerant variety such as Arina could be underlined. The variety resistance constituted a crucial and stable factor for the diseases control. The efficiency of fungicide protection depends on these initial cropping measures as well as on current environmental conditions.