The principles of good agricultural and horticultural practice, which considers both environmental protection and high yielding of plants, require modern methods of cultivation. Cover crops are used in the cultivation of various plants, including root vegetables such as carrot. The purpose of field and laboratory studies was to determine the effect of selected cover crops on the healthiness of carrot (Daucus carota L.). The field experiment took into consideration cover crops such as spring rye, white mustard, buckwheat, fodder sunflower and two systems of soil tillage, i.e.: tillage before winter (ploughing) + spring tillage (a combined cultivator) and only spring tillage (a combined cultivator). In each experimental treatment, the number and healthiness of carrot seedlings were determined. A laboratory mycological analysis made it possible to determine the qualitative and quantitative composition of fungi infecting the underground parts of carrot. Good emergencies and the healthiness of carrot plants were observed in the objects with rye and white mustard as cover crops. The cultivation system had no significant effect on the proportion of diseased seedlings of carrot. Rye and white mustard were more effective than buckwheat and sunflower in limiting the occurrence of fungi pathogenic towards carrot. Diseased seedlings and roots after harvest of carrot were most frequently colonized by Altenaria alternata, A. chartarum, A. dauci, A. radicina, Sclerotinia sclerotiorum, Rhizoctonia solani and Fusarium spp.