Spinocerebellar ataxia-3, (SCA3, also known as Machado Joseph Disease) is a neurodegenerative disease caused by inheritance of a ATXN3 gene containing a CAG repeat expansion, resulting in presence of a polyglutamine (polyQ) repeat expansion within the encoded human ataxin-3 protein. SCA3 is characterized by the formation of ataxin-3 protein aggregates within neurons, neurodegeneration, and impaired movement. In this study we have identified protein aggregates in both neuronal-like cell (SHSY5Y) cells and in vivo (transgenic zebrafish) models expressing human ataxin-3 protein containing polyQ expansion. We have adapted a flow cytometric methodology, allowing rapid quantification of detergent insoluble forms of ataxin-3 fused to a green fluorescent protein. Flow cytometric analysis revealed an increased number of detergent-insoluble ataxin-3 particles in cells and zebrafish expressing polyQ expanded ataxin-3 when compared to cells and zebrafish expressing wildtype ataxin-3. Interestingly, a protein aggregation phenotype could be detected as early as two days of age in transgenic zebrafish, prior to the onset of a detectable movement impairment at 6 days of age, suggesting protein aggregation may be an early disease phenotype in SCA3. Further, treatment of SCA3 cells and transgenic zebrafish with compounds known to modulate the activity of the autophagy protein quality control pathway altered the number of detergent-insoluble ataxin-3 particles detected by flow cytometry. We conclude that flow cytometry is a powerful tool that can be harnessed to rapidly quantify ataxin-3 aggregates, both in vitro and in vivo, and can be utilised to screen and compare potential protein aggregate targeting therapies.