Salinity stress is one of the main obstacles in crop production in many parts of the world, especially in arid and semi-arid regions. Plants' ability to neutralize the effect of salinity largely depends on the internal state K+ and Na+. In fact, maintaining high K+/Na+ ratio in Cytosol is a key element for tolerance to salinity. Rice, one of the most important food crops, a primary food source for more than one-third of the world’ s population. Rice is sensitive to salinity stress, so that, salt effects will extensively damage rice metabolic activities. This study has presented the effects of salinity on some physiological characteristics and genes expression patterns that coded for a number of ion channels in rice. In order to seed germination, the seeds of some cultivar (IR29, Sangtarom, and Jelodar) sterilized and then were placed in germinator. Salinity treatment (120 mM NaCl) were applied 14 days after culture. The leaf and root samples were collected at six time-courses (0, 6, 24, 72, 120 and 168 hours) after sodium chloride stress. Results of physiological assessments showed that the effects of genotype, sampling period and their interactions were significant at 1% level of probability on all measured traits including MALONDIALDEHYDE (MDA), chlorophyll a, chlorophyll b, carotenoids and proline contents. The concentration of chlorophyll a, b and carotenoid of leaves were reduced in early hours of encountering with stress and then increasing the hours of stress, leaf thickness (leaf rolling) caused chlorophyll per leaf unit and increases the amount of chlorophyll. The measurement of MDA in the leaves showed that the greatest increase occurred in sensitive cultivar (IR29). Proline content analysis showed that there was no significant difference between proline content of sensitive and tolerant cultivars under normal condition (no stress), but by exposure to salinity stress, proline content was increased in susceptible more than tolerant cultivar. Proline content in Sangtaroom, as a salt tolerant genotype, has significantly increased in comparison with the control cultivar in 72, 120 and 168 (h) times. Consequently, the responses of sensitive and tolerant rice cultivars to the salinity stress are different from each other and measuring of some parameters such as MDA, chlorophyll a, chlorophyll b, carotenoids, and proline can help to improve the salt tolerance of plants.