A short review on phytochemical analysis of in vitro cultures of selected Polish rare and endangered plants is presented. Analysed secondary metabolites, present in investigated species, are responsible for raw materials medical activity. Phenolic compounds (flavonoids and phenolic acids), secoiridoids, saponins and fatty acids were investigated in micropropagated plants, shoot cultures or callus tissue of eleven plant species from the genera: Gentiana L., Oenothera L., Rubus L., Solidago L., Pinguicula L., Primula L., Eryngium L. The studied species represented medicinal plants or plants used in folk medicine in which the secondary metabolites are usually responsible for their therapeutic properties. The investigations showed that those plants contain pharmaceutically promising compounds. Therefore, plant biotechnology can be used for rapid propagation of rare or endangered plants and the regenerated plants may be used as a source of those rare medicinal plants.