Eyespot, Cephalosporium stripe, and common root rot are soil-borne diseases that damage the stem bases, vascular system, subcrown internodes,and roots of wheat. Resistance in wheat to these diseases is insufficient to prevent significant yield loss when disease is severe. The wheatgrasses Thinopyrum intermedium and Th. ponticum are highly resistant to these diseases. Identification of disease-resistant wheat-Thinopyrum partial amphiploids, chromosome addition, substitution, and translocation lines makes them a valuable source of resistance genes for wheat breeding programs. Single chromosomes or chromosome segments containing resistance genes can be transferred into wheat to produce genetic stocks that afford a better understanding of the genetic control of resistance in wheatgrasses and new genetic resources for wheat improvement. Resistance to eyespot in Th. intermedium and Th. ponticum was associated with the homoeologous group 4 chromosomes, whereas resistance to Cephalosporium stripe was controlled by genes located on chromosomes 3 and 6 of Th. ponticum. Despite the fact that some eyespot- and common root rot-resistant wheat-Thinopyrum lines have blue kernels, resistance is not tightly linked to the blue aleurone trait. Key words: Thinopyrum intermedium, Th. ponticum, eyespot, Cephalosporium stripe, common root rot, Oculimacula yallundae, O. acuformis, Cephalosporium gramineum, Bipolaris sorokiniana