Fusarium head blight (FHB) is one of the most serious diseases of small-grain cereals worldwide, resulting in yield reduction and an accumulation of the mycotoxin deoxynivalenol (DON) in grain. Weather conditions are known to have a significant effect on the ability of fusaria to infect cereals and produce toxins. In the past 10 years, severe outbreaks of FHB, and grain DON contamination exceeding the EU health safety limits, have occurred in countries in the Baltic Sea region. In this study, extensive data from field trials in Sweden, Poland and Lithuania were analysed to identify the most crucial weather variables for the ability of Fusarium to produce DON. Models were developed for the prediction of DON contamination levels in harvested grain exceeding 200 µg kg−1 for oats, spring barley and spring wheat in Sweden and winter wheat in Poland, and 1250 µg kg−1 for spring wheat in Lithuania. These models were able to predict high DON levels with an accuracy of 70–81%. Relative humidity (RH) and precipitation (PREC) were identified as the weather factors with the greatest influence on DON accumulation in grain, with high RH and PREC around flowering and later in grain development and ripening correlated with high DON levels. High temperatures during grain development and senescence reduced the risk of DON accumulation. The performance of the models, based only on weather variables, was relatively accurate. In future studies, it might be of interest to determine whether inclusion of variables such as pre-crop, agronomic factors and crop resistance to FHB could further improve the performance of the models.