Microsclerotia of V. dahliae were placed in the rhizosphere of cotton on the membrane filters. Cotton was cultivated in soil with addition of mineral fertilizers (incidence of disease 85%) and in soil with addition of hydrolysed lignin (incidence of disease 35%). The estimation of V. dahliae growth using method of fluorescing antibodies showed that under conditions leading to severe cotton disease, the quantity of mycelium on membrane filters in the rhizosphere and root colonization were insignificant, however the fungus actively penetrated in cortex already at early stages of cotton growth. Under low incidence of cotton disease V. dahliae formed branched net of mycelium on membrane filters in the rhizosphere, actively colonized root surface, but penetration into root cortex at early stages of cotton growth was insignificant.