Pathogen levels and seed viability of two samples each of barley (Hordeum vulgare) (B1, B2), Canada western red spring wheat (Triticum aestivum) (RS1, RS2), and Canada western amber durum wheat (AD1, AD2) were assessed after heating seed at 50 or 70°C for up to 14 days. RS2 and B2, with an initial incidence of 23 and 84% of Fusarium graminearum, respectively, were also heated at 60°C for 24 days and 80°C for 10 days. Pathogen levels and seed viability were assessed by plating seed onto potato dextrose agar and wet filter paper, respectively. Fusarium graminearum was eliminated from RS2 after 15 days at 60°C, 5 days at 70°C, or 2 days at 80°C. In B2, F. graminearum was eliminated after 21 days at 60°C, 9 days at 70°C, or 5 days at 80°C. After heating at 50 or 70°C, the observed frequency of Cochliobolus sativus in B1 declined slightly but significantly over time, whereas it substantially increased in B2. A significant decline in the incidence of C. sativus was observed in B2 after heating at 80°C. Pyrenophora teres was observed significantly more often in B1 after heating at 50 or 70°C, whereas Pyrenophora tritici-repentis in AD1 and AD2 was unaffected by heating at 50°C. However, the detection of P. tritici-repentis did significantly increase over time in AD2 when heated at 70°C. In AD1, heating at 70°C initially increased, then decreased the observed incidence of this pathogen. Cochliobolus sativus, P. teres and P. tritici-repentis were still viable in the samples after 14 days of heating at 70°C, but C. sativus was not detected after 10 days at 80°C. Germination of wheat tempered to 12, 14, and 16% moisture content was unaffected by heating at 70°C for 7 days, whereas barley tempered to the same moisture content had a slight decline in germination. Germination rates in most samples were unaffected by the treatment times and temperatures sufficient to eradicate F. graminearum, but a significant decline in viability was recorded for AD2 and B1 heated at 70°C. The germination of B2 increased when heated at 70°C, but declined when heated at 80°C. It is recommended that thermotherapy be applied to control national and international movements of F. graminearum and other heat-sensitive pathogens in germplasm used for research and breeding purposes.Key words: thermotherapy, Cochliobolus sativus, Pyrenophora teres, Pyrenophora tritici-repentis.