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Secondary metabolites play an important role in plant protection mechanisms. Presented studies relate to the significant role of some phenolic compounds in health status of sweet pepper plants. Eight cultivars of sweet pepper (‘Barbórka’, ‘Caryca F1’, ‘Mercedes’, ‘Ożarowska’, ‘Podstolina’, ‘Roberta F1’, ‘Robertina’) were investigated in 2007–2009. Flavonoids and phenol acids content in leaves, stems, and roots of sweet pepper plants were analyzed. Flavonoids and phenol acids content was studied using isocratic HPLC method. Disease index of tested cultivars was evaluated in the field. The leaves, stems and roots of pepper were analyzed in the laboratory. The fungi most frequently isolated from pepper were Alternaria alternata, Fusarium spp., Botrytis cinerea, and Sclerotinia sclerotiorum. The highest content of flavonoids and phenol acids was in the leaves of pepper. Flavonoids content in plant parts was positively correlated with the intensity of colonization by pathogenic fungi. Sweet pepper cultivars ‘Caryca F1’ and ‘Roberta F1’ were characterised by low content flavonoids in the tested plant parts and they were colonized by the low number of pathogenic fungi. The cultivars most frequently colonized by pathogenic fungi such as ‘Barbórka’, ‘Podstolina’, ‘Robertina’, had a high content of flavonoids in the tested plant parts. There was no correlation between the content of phenol acids and health status of pepper cultivars.