In the central regions of the Balkan Peninsula, the genus Gentianella is represented by six species. Five of them G. albanica, G. austriaca, G. bulgarica, G. ciliata, and G. crispata were subject of phytochemical and in vitro studies. Two species, G. austriaca and G. bulgarica, were established as shoot cultures and procedures developed for their in vitro propagation. Difficulties with seed germination and precocious flowering affected the final propagation stages. Phytochemical analyses were performed on five species from nature and on cultured shoots. Plant material was rich in secondary metabolites with xanthones, flavone-C-glucosides, and secoiridoids as the principal constituents. The xanthone aglycones, demethybellidifolin, bellidifolin, corymbiferin, and their corresponding glucosides were dominant components in all the species investigated. The predominant substitution pattern of xanthones found in the genus Gentianella was 1,3,5,8 and to a lesser extent, 1,3,7,8. Lanceoside and veratriloside were new compounds found in European Gentianella species. In vitro material generally contained less secondary metabolites than plants from nature; the content of secondary products was influenced by the concentration of benzyladenine (BAP) in the culture medium.