Salt-tolerant wheat lines W4909 and W4910 were derived from a cross between AJDAj5 (a disomic addition line carrying a pair of E^b chromosomes from Thinopyrum junceum) and Ph^I (a line having the Ph^I allele from Aegilops speltoides). Both lines have greater salt-tolerance than their parental lines, which are more salt-tolerant than the common wheat background, Chinese Spring (CS). Genomic constitution of W4909 and W4910 wheat has been estimated at 1.9% and 2.4% non-CS, respectively. Affymetrix GeneChip® Wheat Arrays were used to identify differentially expressed genes in roots and leaves of the above-mentioned five lines under salt stress at EC=30 dS/m. In comparisons to Chinese Spring, W4909 had 39 and 27 whereas W4910 had 52 and 32 differentially expressed wheat unigenes in roots and leaves, respectively. Based on patterns of gene expression in AJDAj5 and Ph^I, those differentially expressed genes in W4909 and W4910 could be attributed to one or the other parent, or both. As expected, there are more genes in W4909 and W4910 that were derived from Ph^I than those from AJDAj5. Transgression gene expression, that might be responsible for higher salt tolerance than both parental lines, was observed in W4910 for nine genes. These results will be useful in developing PCR-based molecular markers for tracing genes introgressed from the Thinopyrum junceum chromosome.