The propensity of proteins to form ß-sheet-rich amyloid fibrils is related to a variety of biological phenomena, including a number of human neurodegenerative diseases and prions. A subset of amyloidogenic proteins forms amyloid fibrils through glutamine/asparagine (Q/N)-rich domains, such as pathogenic polyglutamine (polyQ) proteins involved in neurodegenerative disease, as well as yeast prions. In the former, the propensity of an expanded polyQ tract to abnormally fold confers toxicity on the respective protein, leading to neuronal dysfunction. In the latter, Q/N-rich prion domains mediate protein aggregation important for epigenetic regulation. Here we investigated the relationship between the pathogenic Ataxin-3 protein of the human disease spinocerebellar ataxia type 3 (SCA3), and the yeast prion Sup35, using Drosophila as a model system. We found that the capacity of the Sup35 prion domain to mediate protein aggregation is conserved in Drosophila. Although select yeast prions enhance polyQ toxicity in yeast, the Sup35N prion domain suppressed polyQ toxicity in the fly. Suppression required the oligopeptide repeat of the Sup35N prion domain, which is critical for prion properties in yeast. These results suggest a trans effect of prion domains on pathogenic polyQ disease proteins in a multicellular environment, and raise the possibility that Drosophila may allow studies of prion mechanisms.