AbstractPolyglutamine (polyQ) diseases describe a group of progressive neurodegenerative disorders caused by the CAG triplet repeat expansion in the coding region of the disease genes. To date, nine such diseases, including spinocerebellar ataxia type 3 (SCA3), have been reported. The formation of SDS‐insoluble protein aggregates in neurons causes cellular dysfunctions, such as impairment of the ubiquitin‐proteasome system, and contributes to polyQ pathologies. Recently, the E3 ubiquitin ligases, which govern substrate specificity of the ubiquitin‐proteasome system, have been implicated in polyQ pathogenesis. The Cullin (Cul) proteins are major components of Cullin‐RING ubiquitin ligases (CRLs) complexes that are evolutionarily conserved in the Drosophila genome. In this study, we examined the effect of individual Culs on SCA3 pathogenesis and found that the knockdown of Cul1 expression enhances SCA3‐induced neurodegeneration and reduces the solubility of expanded SCA3‐polyQ proteins. The F‐box proteins are substrate receptors of Cul1‐based CRL. We further performed a genetic modifier screen of the 19 Drosophila F‐box genes and identified F‐box involved in polyQ pathogenesis (FipoQ) as a genetic modifier of SCA3 degeneration that modulates the ubiquitination and solubility of expanded SCA3‐polyQ proteins. In the human SK‐N‐MC cell model, we identified that F‐box only protein 33 (FBXO33) exerts similar functions as FipoQ in modulating the ubiquitination and solubility of expanded SCA3‐polyQ proteins. Taken together, our study demonstrates that Cul1‐based CRL and its associated F‐box protein, FipoQ/FBXO33, modify SCA3 protein toxicity. These findings will lead to a better understanding of the disease mechanism of SCA3 and provide insights for developing treatments against SCA3. image Cover Image for this issue: doi: 10.1111/jnc.14510.