A considerable number of plants from the carnation family (Caryophyllaceae) are known to contain N-glycosidases with cytotoxic properties. This study was intended to investigate the cytotoxic activity of a seed extract from Gypsophila elegans M. Bieb. (Caryophyllaceae). For this purpose, Gypsophila elegans M. Bieb was cultured and seed material was harvested in autumn 2015. Seeds were grinded and defatted by Soxhlet extraction using petrol ether. The defatted seed material was extracted by phosphate buffered saline (PBS). The seed extract showed enzymatic activity against nucleic acid resulting in the fragmentation of hering sperm DNA. In combination with an isolated and characterized triterpenoid saponin from Saponaria officinalis L. the seed extract exhibited a strong cytotoxic activity against glioblastoma cells. This was demonstrated by MTT-based endpoint as well as by impedance- based live cell imaging assays. In order to identify the active principle, the seed extract was analyzed by SDS-PAGE and MALDI-TOF-MS.