In the DOK long-term field trial in Switzerland comparing bio-dynamic, bio-organic, and conventional farming systems, the occurrence of Fusarium species and Microdochium nivale on grains of wheat was investigated from 1997 to 2003. Although no differences between the farming systems were found, the previous crop, the fertilisation level, and the year significantly influenced the disease incidence. In 2003, the effect of the pre-crops potatoes versus silage-maize on fusaria was compared. As expected, the incidence of fusaria was significantly higher after maize compared with potatoes. However, the main responsible species was not F. graminearum but F. poae. This species is known for the production of hazardous toxins. A greater input of fertiliser resulted in a higher incidence of fusaria. In contrast, in the organic systems, the incidence of M. nivale was significantly lower at the higher fertilisation level. Our results demonstrate the need for a detailed monitoring of fusaria and mycotoxins in conventionally and organically grown cereals to define the key factors for the occurrence of different fusaria.