Fusarium head blight (FHB), or head scab, incited predominantly by Fusarium graminearum, causes premature senescence of wheat spikes, kernel damage, and mycotoxin (especially deoxynivalenol, [DON]) contamination of harvested grain, leading to economic losses. In general, there is a positive relationship between DON and FHB, however, this relationship is modified by weather conditions, disease pressure, cultivar resistance, fungicide, pathogen aggressiveness, and interactions among these factors. This relationship is further complicated by the fact that the direct effects of these factors on DON are confounded by their effects on disease. Our goal was to determine the effects of cultivar and fungicide on FHB, fungal biomass (FBM), and DON, and relationships among these variables. Soft red winter wheat cultivars with different levels of Type II resistance to FHB (resistance to fungal spread within the spike) were planted in six field experiments conducted during the 2007, 2008 and 2009 growing seasons. In all experiments, plots were spray-inoculated with a spore suspension of F. graminearum, and in two of the experiments, fungicides (tebuconazole and prothioconazole) were applied at anthesis. Plots were rated for FHB, and spikes were tagged and harvested by disease severity category. DON and fungal biomass were quantified in samples of ground grain from each plot. Linear mixed model analyses were performed to determine fungicide and cultivar effects, and model relationships among FHB, DON, and FBM. There were significant positive linear relationships between FHB and DON; FBM and DON; and FHB and FBM in all experiments, with a significant effect of cultivar on slopes and intercepts in several, but not all experiments. In general, moderately resistant Truman had significantly lower slopes for most relationships, and consistently accumulated less DON and FBM at a given level of FHB than susceptible Hopewell and Cooper. However, at some levels of FBM, DON accumulation tended to be similar among the cultivars. Our results suggest that in Truman, high Type II resistance is associated with high Type III (resistance to DON accumulation) and Type IV resistance (resistance to kernel infection). The effect of fungicides on relationships between FHB and DON and FBM and DON was not significant. However, the main effect of fungicide on arcsine-transformed disease index and log-transformed DON was significant in all experiments, but the effects of cultivar and fungicide x cultivar interaction varied between experiments. Fungicide and cultivar did not have a significant effect on DON accumulation in asymptomatic grain. In some cases, DON in disease-free grain exceeded 2 ppm (a commercially significant threshold) in both fungicide-treated and untreated check plots.