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Mycotoxins are a ubiquitous contaminant and are difficult to prevent or to diminish; it is, therefore, important to establish the contributions of processing steps to eliminating mycotoxins in the production of safer foods. The objective of this study was to investigate the effects of wheat cleaning, sorting, and milling processes on Fusarium mycotoxin distribution in two naturally contaminated wheat cultivars. The study focused on evaluating the effects of first-stage processing methods, cleaning, and gravity separator, on wheat mycotoxin content. The distribution of Fusarium mycotoxins was analyzed after two milling processes. Firstly, a Laboratory Mill 3100 was used to obtain the whole milled wheat. Secondly, a pilot-scale mill Quadrumat Senior was used to get wheat milled fractions (finished flour and bran). Wheat samples (BRS Parrudo and BRS 374) were collected during the 2014 season that were highly vulnerable to Fusarium outbreaks in Southern Brazil. Fusarium toxin (DON, 3-ADON, 15ADON, NIV, and ZON) levels were determined for all milled fractions via chromatography (UHPLC-MS/MS). The cleaning and sorting methods employed post-harvest significantly reduced the mycotoxin content in wheat. The reduction of mycotoxin was progressive through each processing method, and the gravity separator equipment resulted in the lowest contamination levels in products intended for human consumption for both cultivars. Through the milling process, the DON contamination in finished flour was significantly lower than in milled wheat; however, there were no significant differences in contamination between the milled wheat and bran. The cleaning and sorting methods for both wheat cultivars generated safer foods when compared with unsorted wheat samples (BRS Parrudo and BRS 374)., http://www.sciencedirect.com/science/article/pii/S0956713515301195