Fusarium Head blight (FHB) is a destructive disease causing considerable yield loss in wheat (Triticum aestivum L.). Grain produced from the infected head is shriveled and kernels are commonly contaminated with the mycotoxin deoxynivalenol (DON). Selection for either low spread or low incidence of the pathogen in inoculated plots often results in reduced accumulation of DON in the grain, however, variation in DON content within resistant classes can be significant, suggesting DON accumulation and phenotypic resistance may be conditioned by independent genes. ‘Ernie' winter wheat is moderately resistant to FHB. The objective of this study was to identify QTL associated with DON content in a set of 243 recombinant inbred lines (RILs) developed from the cross Ernie/MO 94-317 and determine if these differ from four QTL that have been associated with type II resistance in the same population. Plants were arranged as a randomized complete block design with four replications (8 plants per RIL per replication) and point-inoculated in the greenhouse with Fusarium graminearum. Kernels from inoculated heads of each RIL were hand-threshed, ground, and assessed for DON content. Preliminary data identified three QTLs associated with low DON content on chromosomes 3BS, 4BL and 5AL that together account for 20% of the phenotypic variation. The QTL on 3BS was in the same region as a minor QTL in Ernie conditioning type II resistance, however, QTL regions on 4B and 5A appear to be independent of QTL on those chromosomes associated with type II resistance. Additional studies are required to confirm these findings but based on these results, wheat breeders may need to pyramid resistance QTL with those for low DON to minimize DON content in resistant varieties.