Foxtail millet (Setaria italica (L.) P. Beauv.) is an ideal crop for changing climates and stressed environments due to its short duration, high photosynthetic efficiency and good level of resistance to pest and diseases. Soil salinisation is an increasing problem, with 23% of the global cultivated land already affected. Foxtail millet has potential as a crop for salt-affected soils, with its high tolerance to salinity. The foxtail millet core collection (n = 155) was screened in a soil saturated once with 100 mm NaCl and in a non-saline control in 2008 and a subset (n = 84) in 2009 in a partly controlled environment using Alfisol to identify the best salt-tolerant germplasm. Plants were grown in pots and protected from rain. The salinity response was measured as grain yield per pot. Genotype and salinity × genotype interaction effects were significant for most traits, and there was a large range of yield and biomass variation across accessions. Salinity delayed panicle emergence and maturity, and reduced shoot biomass by 24–41% and grain yield by 7–30%. Salinity did not reduce the harvest index. Among the plant components, stem biomass was reduced most by salinity. There was a large variation in grain yield and other traits among the genotypes in the saline pots. The yield loss by salinity was associated with duration of crop growth, and grain yield loss was highest in the early-maturing accessions. All accessions were grouped into five sets based on grain yield under saline conditions, and the most highly tolerant group had 13 accessions. The salinity-tolerant accessions can be useful parents once their performance is confirmed under saline field conditions.