Foliar and stem diseases of annual Medicago spp. caused by Phoma medicaginis and Leptosphaendina trifolii can not only reduce yield, but also affect herbage quality by inducing the production of the phytoestrogen coumestrol. To determine differences in host reaction to these pathogens, 33 cultivars and lines in 1993 and 10 cultivars in 1995 were evaluated in inoculated field tests. In the 1993 test, a number of genotypes with high levels of resistance to leaf and stem disease caused by P. medicaginis and to leaf disease caused by L. trifolii were identified. Genotypes with very high levels of resistance to stem disease caused by R medicaginis were M. sphaerocarpos GRC5659.4.1 and SAD10069, M. murex GRC87.1, GRC707, and GRC708, M. truncatula Z771, and M. solerolii DZA3180.1, all of which had stem disease scores of <= 1.0 (scale 0 to 10) by the end of the growing season. The levels of cournestrol produced ranged from 114 to 1.230 ppm dry weight in stems across the genotypes, and the score for stem disease caused by P. medicaginis in the corresponding cultivars ranged from <= 0.8 to 8.9, respectively. The 1995 test confirmed the relative responses of nine cultivars (Caliph, Circle Valley, Cyprus, Harbinger AR, Zodiac, Paraggio, Santiago, Serena, and Orion) of annual Medicago spp. to leaf and stem disease caused by P. medicaginis and to stem disease caused by L. trifolii. Those with the lowest levels of cournestrol in the stems were M. solerohi DZA3180.1, M. truncatula Paraggio, and M. sphaerocaipos SAD10069, all with levels : 130 ppm. The highest level was found in M. polymorpha SA4178 (1,230 ppm). M. littoralis Harbinger AR, Z286, Z298, and Z912, M. murex 89F16.1.1. M. orbicularis SA8460, and M. polymorpha SA4188, all had cournestrol levels of > 600 ppm. For stem disease caused by P medicaginis in particular, there was significant correlation of the level of disease with the level of cournestrol in stems at the end of the growing season. In contrast. for L. trifolii, there was significant negative correlation (leaf disease) or only a weak positive correlation (stem disease) with cournestrol in stems at the end of the growing season. Incorporation of these identified disease resistances into commercial cultivars offers a promising avenue not only as a long-term strategy for management of foliar diseases in annual Medicago spp., but also as a means of reducing phytoestrogen levels in commercial annual Medicago spp. pastures in order to minimize the adverse effects of phytoestrogens on fertility levels in sheep.