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Fusarium head blight (FHB) of wheat, mainly caused by Fusarium graminearum, is a major wheat disease globally, causing significant yield and quality losses. Additionally, infection with leaf rust (LR), stem rust (SR) and stripe rust (YR) caused by Puccinia triticina, P. graminis f. sp. tritici, and P. striiformis f. sp. tritici, respectively, leads to significant yield losses under favourable conditions. The use of cultivars with increased resistance is considered an effective tool for FHB and rust disease management. The improvement of agronomic traits in winter wheat is also crucial to meet global food demand. The objectives of this study were to: i) identify QTL associated with FHB resistance in two doubled haploid (DH) winter wheat populations D8006W/Superior and Triumph/25R51, ii) identify QTL associated with LR, SR, and YR resistance in the Triumph/25R51 population, and iii) identify QTL associated with agronomic and quality traits in the Triumph/25R51 population. The evaluations of FHB, and agronomical traits were performed across multiple site years representing both Eastern and Western Canada. Three rust diseases were evaluated in respective trials across multiple site years. Genotyping of both DH populations was performed using the 90K Illumina Infinium iSelect single nucleotide polymorphism (SNP) array followed by linkage map construction using high quality SNP makers and QTL analysis. Major FHB resistance QTL were detected on chromosomes 1A, 1B, 2D, 4B, 5A and 7A for the D8006W/Superior population and on chromosomes 2A, 2D, 3B, and 7D for the Triumph/25R51 population. The FHB QTL on chromosome 2D in both populations was associated with plant height and days to anthesis QTL. The major FHB resistance gene, Fhb1, was associated with FHB resistance in the Triumph/25R51 population. Rust resistance QTL were detected on chromosomes 1B, 4A, 5B and 7B for LR, chromosomes 1B, 4B and 6A for SR and chromosomes 1A, 4B and 5B for YR. Agronomical traits QTL were detect