In Canada, very little is known about fusarium head blight (FHB) and leaf rust on rye. The overall goal of the thesis is to provide critical and practical information on rye reaction to FHB, leaf rust, and ergot, and the effect of fungicide application on controlling FHB. Fall rye spikes were collected from naturally infected fields in Manitoba. Five Fusarium species (Fusarium graminearum, F. avenaceum, F. poae, F. sporotrichioides, and F. equiseti) were isolated and identified from these samples. Fusarium graminearum was the principal Fusarium species recovered from affected kernels. It was the most pathogenic species among the four Fusarium species (F. graminearum, F. avenaceum. F. sporotrichioides, and F. poae) evaluated on six fall rye genotypes and two wheat checks in the greenhouse. Two sets of fall rye genotypes were assessed through artificial inoculation in multi-environmental trials. Rye was less affected by FHB and more resistant to the disease than winter wheat. Disease levels and deoxynivalenol (DON) varied among fall rye genotypes tested for their reactions to F. graminearum. Fourteen open-pollinated genotypes, nine hybrids, and eight testcross hybrids showed high FHB resistance. Few genotypes had low ergot severity under natural infection. The fungicide Prosaro™ (prothioconazole and tebuconazole) application timing for managing FHB on rye was investigated through six treatments, including application at heading, 10% anthesis, 80% anthesis, six days after 50% anthesis, and inoculated-untreated and uninoculated-untreated controls. The highest percent control of FHB incidence, severity, and index occurred when fungicide was applied at 10% anthesis, while fungicide applied at 80% anthesis resulted in the highest efficacy for reducing Fusarium-damage kernels and DON. Fungicide treatments significantly increased thousand kernel weight, test weight, and yield under a high mean FHB index. Two sets of fall rye genotypes to leaf rust was evaluated in rust nurseries through artificial inoculation. Most of the open-pollinated genotypes were moderately susceptible or susceptible to leaf rust. Several hybrids showed moderate resistance or resistance to leaf rust with low disease severity. The integrated information from this study will assist rye growers manage FHB, leaf rust, and ergot, and provides vital information for resistance breeding.