Crop rotations are known to be a natural barrier against a wide range of fungal soil-borne pathogens. Results shown in this paper are based on observations that were made in the third growing period of a 3-year cereal crop rotation (1989–1991). Mixtures as pre-crops and main crops were compared with pure stands of barley and wheat also grown as pre- and main crops. After this 3-year period, field experiments showed that interspecific mixtures of winter barley and winter wheat reduced stem rot caused by Pseudocercosporella herpotrichoides, Fusarium spp., Gaeumannomyces graminis and Rhizoctonia cerealis. Growing barley and wheat after a cereal mixture resulted in an increased number of healthy plant stems. The pre-crop mixture significantly reduced the disease incidence of Fusarium spp. on barley (> 50%) during stem elongation and ripening. Disease incidence of G. graminis on barley during ripening decreased from 44% after barley to 9% when grown after the mixture. Differences in take-all incidence on wheat due to different pre-crops were not significant. The percentage of P. herpotrichoides lesions on wheat grown in a mixture increased after pre-crops containing barley. Furthermore, interactions occurred between pathogens, indicating differences in competition. Additional effects on plant health were observed where barley-wheat mixtures were grown for 2 years. In general, the incidence of stem base diseases was lowest in mixtures that were grown after a mixture. Disease reductions on wheat grown in a mixture after a mixed pre-crop were comparable to those disease reductions brought about by chemical fungicides applied in pure stands of wheat. Pathogen frequency on wheat hypocotyl and root tissue was estimated using a selective medium: the frequency of G. graminis on wheat tissue decreased from 14% after the pre-crop barley and 7% after the pre-crop wheat, to 1% after the pre-crop mixture. The frequency of Fusarium spp. was generally not affected, but the spectrum of species changed quantitatively. A greater number of weak or non-pathogenic fungi were isolated from wheat segments when the plants were grown after a mixed pre-crop.