The paper presents an analysis of yielding of winter wheat in different crop production systems (ecological, conventional, integrated). The research was conducted during 10 years. The occurrence and intensity of different factors limiting the level of yielding (weed infestation, stem base and leaf diseases and changes of soil fertility) were taken into account in the research. The largest yields of winter wheat were recorded in the integrated system, whereas the smallest in the organic system and in monoculture of winter wheat. The yields in monoculture were the most variable. Stem base and root diseases were the main factors influencing low productivity of winter wheat in monoculture. Whereas, in the organic system leaf diseases and deficient nutrient status were responsible for smaller yields. In the analysed period no distinct changes in soil fertility were observed. At the beginning of the research period a decrease of potassium content in soil was observed in the organic system, however, due to permanent monitoring of potassium content and application of fertilizers approved in the organic agriculture this tendency was reversed. In the conventional system and in monoculture of winter wheat a decrease of organic carbon content in soil was observed.