There is growing interest in malting and brewing with rye. However, previous research has shown a propensity for the development of deoxynivalenol (DON) in rye malts, even when levels on the grain is low. The main objective of this study was to assess the growth of F. graminearum and development of trichothecenes during malting of rye. Infected samples were obtained from 2016 variety trails in Minnesota. While DON levels were generally below 0.2 mg/kg, an average increase of 41 % was seen after malting. The most significant increases in DON were at three days of germination. Fusarium Tri5 DNA levels were observed to increase at two days. When single kernels were tested, most were free from DON. Levels in the bulk grain sample were due to a small number of highly contaminated kernels. In the malted samples, a greater portion of kernels contained DON, and overall levels were much higher.