To understand the mechanisms underlying acquisition of resistance to salinity, we recently produced calli of Medicago truncatula resistant to NaCl-induced salt stress following application of a step-up recurrent selection method. The effects of salinity on cell size are known but those on cell morphometry were never studied before, and this work fills that gap. Suspension cultured cells of M. truncatula R108 and Nicotiana tabacum BY-2 resistant to increasing NaCl concentrations up to 150 mM NaCl were used. The cell and nuclear surface area and position of nuclei within cells were measured. The surface area of salinity resistant cells of Medicago truncatula R108 and Nicotiana tabacum BY2 and their nuclei, produced by step-up recurrent selection, were reduced, and cells elongated as NaCl increased, but these parameters were unreliable in explaining cell survival and growth at high NaCl. Conversely, nuclei of resistant cells migrated from the centre to the periphery of the cytoplasm close to the walls. Nuclear marginalisation was for the first time observed as a result of salt stress in plant cells, and could be a novel helpful morphological marker of acquisition of salinity tolerance.