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The effect of a highly virulent fungus Verticillium dahliae Kleb. VD-11, with non-defoliating strain on polyphenol oxidase (PPO) and the antioxidant enzymes, such as guaiacol peroxidase (POX) and superoxide dismutase (SOD), was studied in double haploid cotton variety-Pima 3-79 (Gossypium barbadense L.), highly inbred line TM-1- (Gossypium hirsutum L.), as well as in genotypes CS B-15 and GS B-22, created by the substitution of one chromosome of TM-1 with the chromosome 15 and 22 of Pima 3-79 respectively. The treatment of plants with the pathogen led to an increase in the activity of PPO approximately 1.2 times in the case of TM-1 and CS B-15. However, these changes were insignificant in the case of Pima 3-79 variety, whereas the activity of the enzyme in the case of CS B-22 was decreased apparently. Similar effects were also obtained for POX. After inoculation, the activity of SOD in all genotypes, except CS B-15, was increased. On the contrary, the activity of SOD was decreased in the case of CS B-15 genotype. It was found that plant infection with the pathogen leads to a change in the concentration of free radicals, which, in turn, affects the activity of antioxidant enzymes. The fungal infection also led to the creation of new paramagnetic centers and nanophase crystal-like iron oxide particles in roots, but not in leaves. [ABSTRACT FROM AUTHOR]