Fusarium head blight of wheat is caused by the Fusarium species that produces mycotoxins, such as deoxynivalenol (DON). The distribution of DON in wheat products can lead to high economic and health impacts. The objective of this study was to evaluate the natural distribution of DON in the wheat milling process and wheat-based products, as well as the daily intake estimates for the Southern Brazilian population. The fractions of wheat grains (milled wheat, finished flour and bran) were produced in a mill. Additionally, wheat-derived products, such as pasta, bread and crackers were analyzed. The bran fraction had the highest mean concentration of DON (2278 μg kg−1), followed by milled wheat and finished flour (1895 μg kg−1 and 1305 μg kg−1). The distribution factor in the finished flour (69%) fraction demonstrates that DON was reduced when compared to milled wheat, by contrast of bran fraction that presents higher DON levels (120%). A percentage of 35% bran, 35% finished flour and 30% milled wheat samples would not be in compliance with future Brazilian regulations for DON levels. From the wheat-based products analyzed, 17% of whole bread and 10% of salted cracker products were contaminated with DON, with a median of 437 μg kg−1 and 624 μg kg−1, respectively. The finished flour was the fraction that most contributes to the daily intake of DON in Southern Brazil, representing 89.6% of the provisional maximum tolerable daily intake.