Stem rust (caused by Puccinia graminis Pers.:Pers. f. sp. tritici Eriks. & E. Henn.), a devastating disease of wheat (Triticum aestivum L.), was effectively controlled worldwide for the past 50 yr by deployment of stem rust resistance (Sr) genes in wheat cultivars. However, a new stem rust race, TTKSK (known as Ug99 or TTKS) that emerged in eastern Africa, is a cause of concern because it has broad virulence to currently deployed Sr genes. To identify potentially new sources of effective Sr genes against Ug99, we evaluated and characterized the seedling responses to TTKSK of 62 wheat lines derived from crosses of common or durum wheat (T. turgidum L. ssp. durum) with the species Thinopyrum junceum, Th. intermedium, Th. bessarabicum, Th. elongatum, Th. ponticum, Elymus rectisetus, Aegilops caudata, and Ae. speltoides. For stem rust evaluation, we first tested all lines for reactions to races TTTT and TTKSK. Lines initially showing resistance to TTKSK were then retested with eight races, including three races in the TTKS lineage (TTKSK, TTKST, and TTTSK) and five North American races (QFCS, QTHJ, RCRS, RKQQ, and TPMK). Thirty wheat-alien species derivatives had resistance to TTKSK, TTKST, and TTTSK. The comparisons of wheatalien species derivatives and their parental lines for reactions to different races suggested that 12 partial amphiploids or amphiploids and four disomic addition lines may carry novel genes for stem rust resistance. These resistant lines represent materials for introducing stem rust resistance genes into wheat breeding.