In the paper the results concerning occurrence of fungal diseases on selected varieties of winter wheat and one variety of spelt wheat cultivated in the organic crop production system were presented. The research was conducted on a special field experiment located in the Experimental Station of IUNG-PIB in Osiny in which different farming systems have been com-pared since 1994. Evaluation of the intensity of infestation of roots, stem base and leaves of winter wheat was done in three development stages. Winter wheat cultivated in the organic system was less infested by stem base diseases than wheat cultivated in the conventional system. However leaf diseases, mainly: brown rust and septoria leaf spot dominated in the organic system. Infestation of stem base and leaves of officially registered varieties was low, whereas "old" varieties were significantly more infested.