Common centaury, Centaurium erythraea Rafn., represent the best known and the most investigated medicinal plant species of genus Centaurium. Centaury has been used for centuries in traditional medicine. Secondary metabolites such as bitter secoiridoid glucosides (gentiopicrin, swertiamarin and sweroside), xanthones (eustomin and demethyleustomin), and phenolic acids are the main constituents responsible for the therapeutic properties of centaury. Previous investigation showed that overexpression of the AtCKX genes in transgenic centaury plants did not result in a decrease of total cytokinin (CK) content, but in an altered CK profile leading to a decline of bioactive, the most important physiologically active group of CKs.The aim of this study was to investigate antibacterial and antifungal activity of transgenic centaury methanol extracts as well as pure secoiridoid and xanthone compounds on four Gram positive, four Gram negative bacteria and eight species of microfungi. All tested methanol extracts of control and transgenic AtCKX1 centaury shoots and roots showed better antibacterial activity, while pure compounds (gentiopicrin, swertiamarin, eustomin and demethyleustomin) showed better antifungal activity. The results obtained in this work suggest that centaury methanol extracts and pure compounds represent potential antimicrobials confirming the possibility of using these compounds in agronomy, veterinary, medicine or food industry.