Carrot culrivars ‘Bolero’, ‘Fayette F1’, ‘Flakke, Koral’, ‘Nantes’, ‘Perfekcja’ and ‘Sukces’ were grown in integrated and organic farming systems. The severity of Alternaria leaf blight and root diseases was evaluated at harvest and after five months of storage. Fungi were isolated from carrot roots. Disease severity was affected by the years of the study, farming system and cultivar. The severity of Alternaria leaf blight was lower in the integrated farming system than in the organic system. Carrots of cvs. ‘Bolero’ and ‘Fayette F1’ were healthiest. In both production systems, the symptoms of mixed rot (soft rot, Pectobacterium carotovorum subsp. carotovorum and Sclerotinia rot, Sclerotinia sclerotiorum), dry rot (Fusarium spp.), common scab (Streptomyces scabies), crater rot (Rhizoctonia carotae) and black rot (Alternaria radicina, A. dauci) were encountered sporadically, and their severity was low on carrot roots analyzed at harvest. Disease symptoms became more severe during storage, and they were more frequently observed on carrot roots in the organic farming system. Cultivars exerted varied effects on the severity of the analyzed root diseases. The fungal pathogens isolated from carrot roots confirmed the presence of disease symptoms.