Investigations were carried out in 2007-2009 on the plots of the Felin Experimental Station belonging to the University of Life Science in Lublin. The studies comprised two cultivation lines of durum wheat (Triticum durum L.): STH 716 and STH 717, as well as the 'Tonacja' cultivar of common wheat (T. aestivum ssp. vulgare L.). Two levels of chemical protection were applied in the cultivation: minimal and complex protection. Infection of wheat roots and stem bases was recorded in each growing season at hard dough stage (87 in Tottman's scale, 1987). After three years of study, the mean disease indexes for the analyzed wheat genotypes in the experimental treatment with minimal protection were 31.13, 30.43 and 38.83 for, respectively, the 'Tonacja' cultivar and the cultivation lines of T. durum STH 716 and STH 717. In the experimental combination with complex protection, after three years of study the disease indexes ranged from 25.26 (T. durum STH 716) to 30.83 (T. durum STH 717). The results of mycological analysis of diseased plants showed that Fusarium spp., especially F. culmorum, F. avenaceum as well as Bipolaris sorokiniana and Rhizoctonia solani, caused root rot and necrosis of wheat stem bases. The analyzed chemical protection levels did not significantly influence grain yield of the investigated genotypes of T. aestivum and T. durum.