Based on a 2-year field trial at two locations in Lower Saxony (Germany), 395 Fusarium isolates belonging to 13 species were collected from more than 3,000 sugar beet roots that were apparently healthy at harvest. In a comparative screen, subsamples were analyzed for Fusarium infection directly after harvest and after different storage conditions. Depending on the storage duration, a different species composition was observed. F. redolens was predominant in freshly harvested beets, while F. culmorum, F. cerealis, and F. graminearum comprised 50.0% (2006) and 84.8% (2007) of the Fusarium mycoflora of sugar beets subjected to long-term pile storage. Randomly selected isolates of all species detected were tested for pathogenicity to sugar beet, but only isolates of F. graminearum and F. sambucinum caused severe root symptoms. Overall, 34 isolates of all species detected were characterized for their mycotoxin profile in rice culture to determine potentially produced toxins for future analysis of sugar beet. A total of 26 Fusarium mycotoxins were detected by liquid chromatography-tandem mass spectrometry, including trichothecenes, zearalenone, and especially high amounts of beauvericin, enniatins, and moniliformin. Further work is required to analyze the natural occurrence of these mycotoxins in sugar beet.