Endopolyploidy is a condition of a cell containing reduplicated genetic material in its nucleus. Cells with the nuclei of different ploidy levels are often present within a single polysomatic organism. Endoreduplication is thus a modified cell cycle that omits cytokinesis and leads to chromatin replication in the endopolyploid cells. This study aimed to research the effect of salinity on endopolyploidy of Trifolium pratense and T. repens. Both species are important pasture legumes and belong to the genus Fabaceae with the well documented endopolyploidy occurence. Endopolyploidy levels in the seedlings treated with 0, 30, 60, 90 and 120 mM NaCl were investigated by flow cytometry. The seedling organs were evaluated during three ontogeny stages. The cytometric data plotted on a histogram showed the presence of 2C-16C nuclei in T. pratense and 2C-8C in T. repens. The hypothesis that salinity induces additional endocycles was not confirmed. Our results show that the distribution of nuclei among ploidy levels does not differ markedly between the treatment groups and the control ones. Additionally, only minor changes were observed among the endoreduplication indexes (EI) of plant organs after exposure to various salt concentrations. Endopolyploidy patterns within the salt-treated seedlings during ontogeny are similar to the controls. We suggest that endopolyploidy in Trifolium species is a conserved genetic trait, rather than an adaptation to salinity stress. The analyses of the roots of T'. pratense at stage III show that with the increased concentrations of NaCl the length of roots decreased, but no evident changes in endopolyploidy occured.