Abstract Millets are important agricultural crops for arid regions due to short life span and their resistance to salinity and drought conditions. In Iran, three main species of millets including proso millet (Panicum miliaceum), foxtail millet (Setaria italica) and pearl millet (Pennisetum glaucum) are cultivated in Shouthern Khorasan province, eastern Iran. In order to assess inter-specific genetic variation for salt tolerance at vegetative and reproductive stage, an experiment was conducted in split plot based on completely randomized block design. Nine genotypes of these millets collected from four different regions of the Shouthern Khorasan province (Ghaen, Sarayan, Nehbandan, and Birjand) were subjected to three levels of salinity stress (1.5, 5.5, and 9.5 dS/m). Although the yield and other yield related parameters of millets decreased by salinity stress, this reduction was more prominent only at high level of salinity (9.5 dS/m). Remarkable differences among same species from different areas were observed. Growth and yield capacity of three millet species from Birjand were also different. Of three millets, pearl millet from Birjand followed by foxtail millet, showed maximum yield potential under both salt stress and normal conditions. Of genotypes of foxtail millets, genotype from Sarayan exhibited maximum growth and yield potential under saline conditions. In contrast in proso-millets, genotype from Ghaen showed higher salt tolerance. Thus, salt tolerance varies in three millets from different regions, which could be further explored in future research.