Rye is considered as a very healthy crop but is not completely free of diseases such as soil-borne diseases, ergot, brown rust and Rhynchosporium. Snow mould, powdery mildew, black rust and soil-borne viruses vary in their regional significance. Brown rust, Rhynchosporium and powdery mildew are the most important diseases nationwide. However, they can be successfully controlled by fungicide treatments. Thanks to plant breeding, rye varieties with good brown rust resistance are now available. Fusarium head blight susceptibility is classified as being low in rye. Premature bleaching symptoms usually only occur on single spikelet’s. Infection of complete ear rows or even of the total ear does not occur naturally in rye. Snow mould can cause considerable winterkill. Only seed-born infestation can be controlled by seed treatments. Black rust is a dangerous pathogen that can occur in Germany and Austria during hot and droughty conditions. Damages can be severe as the fungus infests the stem and thus significantly restricts water and nutrient transport. Ergot infection is problematic. Deductions are made if rye for human consumption exceeds at delivery. Only batches with an ergot content of no more than 0.05 % by weight can be marketed as baking rye without deductions; for rye as animal feed the maximum threshold is 0.1 %. Contaminated harvested crops must be cleaned. Ergot should be completely avoided in the food chain. Variety choice is only one influencing factor but in years favouring infection it is far from being sufficient to control the problem. A range of measures must be taken including appropriate cultivation measures and in particular thorough cleaning carried out by the dealers.