A field experiment was conducted in 2007–2008 at the Brody Experimental Station of Poznań University of Life Sciences. The aim of this study was to determine leaf and stem base disease severity on winter triticale as an effect by cropping systems and fertilization. Pseudocercosporella herpotrichoides, Fusarium spp. and Gaeumannomyces graminis occurring on stem bases and roots were found in winter triticale. The incidence of stem base and root diseases was shown to increase under monoculture in comparison with crop rotation. Stem base and root diseases severity was lower after farmyard manure and NPK + Ca application than after mineral fertilization NPK. The farmyard manure + NPK fertilization increased the incidence of leaf and ear diseases of winter triticale in relation to the other fertilization treatments.