The complex nature of plant resistance to adverse environmental conditions, such as salinity and drought requires a better understanding of the stress-induced changes that may be involved in tolerance mechanisms. Here we investigate stress-related morpho-physiological effects during vegetative and reproductive growth in two Japonica rice cultivars (Bomba and Bahia) exposed to a range of NaCl concentrations from the seedling stage. The stress-related detrimental effects were observed either earlier or to a higher extent in cv. Bomba than in Bahia. Damages to the photosynthetic apparatus were related to loss of chlorophyll (Chl) and to a decrease of the maximum potential efficiency of PSII (Fv/Fm), affecting negatively net CO2 assimilation rate (PN). Stress-related leaf anatomical alterations were analysed during the vegetative and reproductive stages. The size of bulliform cells as well as dimensions related to the vascular system increased under mild stress but decreased in the longer term or under higher stress level. The pattern of the anatomical alterations observed at the reproductive stage under 20 mM NaCl was reflected in poor panicle development and yield loss, with effects more pronounced in cv. Bomba than in Bahia. In summary, our results show that some physiological and, particularly, leaf anatomical responses induced by NaCl stress are distinctive indicators of sensitivity to salt stress in rice cultivars.