This work is a long-term (1998–2015) study of root rot in the six-field crop rotations of various types, with varying degrees of saturation of crops. It is shown that saturation of crop rotation by crops leads to the accumulation of infection in the soil increases the development of root rot of cereals. The use of clover in crop rotation can significantly reduce the incidence and progression of the disease and creates the preconditions for phyto-sanitary improvement of agro-ecosystems.