Micromorphological and chemical analyses of the leaves of soft wheat hybrids, differing in susceptibility to brown rust damage (pathogen Puccinia triticina Erikss.), were carried out. In this work we studied F4 progeny samples obtained by crossing the Novosibirsk 9 common wheat variety with Chinese Spring null-tetrasome lines, with differences in the CAD isozymes pattern and affected by fungal infection by 10–20, 30 and 70%. The leaves of typical plants of each genotype that were not exposed to infection were analyzed. The ratio of inorganic substances – potassium and calcium salts, and biogenic silicon oxide – was determined both on the surfaces of the leaves and in there total biomass. It is established that silicon oxide, which prevails on the surface of the leaves, increases resistance to fungal infection. Based on TGA, the lignin structure of leaves affected by brown rust is uniform. Lignin of the leaves of the resistant genotypes has several fractions that differ in their thermal properties. The content of glycosides of apigenin and aromatic acids is higher in the leaves of resistant genotypes. The leaves of plants susceptible to fungal infection contain less chlorophyll b, which could cause a delay in growing and flowering and weaken the protective reactions of plants.