Embryonic root is the primary site of salinity perception in germinating seeds. To understand better the NaCl stress response of lupine embryo axes, ultrastructural approach combined with analysis of DNA degradation was used. In this study lupine embryo axes were cultured in vitro on the medium supplemented with two salt concentrations 250 and 500 mM to differ the reaction. To assess the rate of DNA damage, alkaline electrophoresis of isolated nuclei and DNA fragmentation analysis were performed. Results of these studies suggest programmed cell death induction under salinity stress. Moreover, ultrastructure observations revealed other characteristic features of programmed cell death like endoplasmic reticulum reorganization, increased level of vacuolization, chromatin condensation and starch grains degradation. Our comparative analysis of ultrastructure changes and DNA fragmentation speak in favour of programmed cell death in lupine (Lupinus luteus L. 'Mister') embryo axes treated for 12 h with 250 and 500 mM NaCl.