Selenium is of micronutrients which beside its effective role on increment of endurance of plants such as rice against undesirable environmental effects, plays an important role in human health, due to its anti-oxidant and anti-cancer characteristics. Thus, to evaluate the influence of selenium on diminishing the negative effect of salinity and low seed storage in germination of Shafagh rice cultivar (CV. Shafagh) a factorial experiment was carried out based on completely randomized factorial design (CRFD) with three replications at the Physiology Lab of Shahid Chamran University in 2012. Testing factors included pretreatment of seeds with selenium in 0 and 16 mg/l, salinity in three levels including 0, 6, and 12 dS/m, and seed grain weight of 22, 24, and 26 gr. Results showed that salinity stress caused drastic and significant damage on measured properties of rice germination as much as 32 to 59 % in germination indices and 30-60% in germination characteristics. Priming with selenium rectified the salinity damage (1-23%) and low seed grain weight (32-47%) significantly, so that the germination rate in control treatment was classified in the same statistical group with selenium treatments and seed grain weight of 24 gr and also rice primed with selenium and salinity of 6 dS/m. Accordingly, salinity value and low seed weight had a drastic negative effect on all measured properties, but selenium pretreatment rectified the damages on germination through the increment of anti-oxidant enzymes.