Cover crops and antagonistic fungi have a very positive effect on the soil environment. Such cover crops as oats, rye, common vetch, tansy phacelia, white mustard, sunflower and fodder radish can be used in the cultivation of different species of vegetables. They increase the biological activity of the soil by stimulating the growth and development of microorganisms antagonistic and can protect cultivated plants from soil-borne phytopathogens. The purpose of the field and laboratory studies was to determine the antagonistic activity of selected fungi species occurring in the soil under carrot cultivated with the use of oats, tansy phacelia and spring vetch as cover crops. The healthiness of the roots of this vegetable was also investigated. Cover crops contributed to the increase of the population of antagonistic fungi (Trichoderma spp., Clonostachys spp., Myrothecium spp. and Penicillium spp.) in the soil. Regardless of the experimental treatment, those antagonistic fungi were most effective in limiting the growth of Sclerotinia sclerotiorum, Alternaria dauci and A. radicina. The effect of those fungi was a little smaller towards Fusarium oxysporum and Rhizoctonia solani. Oats and spring vetch were most effective in limiting the occurrence of soil-borne fungi. Cover crops had a positive effect on the healthiness of carrot roots. Alternaria dauci, A. alternata, A. radicina, Fusarium oxysporum, Globisporangium irregulare, Neocosmospora solani, Phytophthora sp., Rhizoctonia solani and Sclerotinia sclerotiorum proved to be the most harmful towards the studied underground parts of carrot. Oats proved to be the most effective in inhibiting the occurrence of the pathogenic fungi for Daucus carota L.