Spinocerebellar ataxia 2 (SCA2) belongs to the group of neurodegenerative diseases caused by expansion of a polyglutamine (polyQ) domain. Overexpression of mutant ataxin-2 causes cell death and Golgi dispersion in cell culture as well as morphologic and functional changes in mouse models. To further define the mechanism of ataxin-2 induced cell death, we compared the cytotoxic effects of different domains of normal and mutant ataxin-2. N-terminal truncated ataxin-2(N) with expanded polyQ repeats did not form intranuclear inclusion and was less cytotoxic than the corresponding full-length ataxin-2. Ataxin-2(del42)[Q22], which lacks 42 amino acids (aa) within the Lsm-associated domain (LsmAD) necessary for Golgi localization, showed a diffuse cytoplasmic localization and was more toxic than wild type ataxin-2[Q22]. Mutant ataxin-2(del42)[Q108] displayed the same toxicity as ataxin-2[Q108], but did not disperse the Golgi apparatus to the extent seen with full-length mutant proteins. These observations confirm that ataxin-2 cytotoxicity increases with increasing polyQ expansion and Golgi dispersion and indicate that, in contrast to other polyQ diseases, N-terminal fragments containing the polyQ repeat are less toxic than full-length ataxin-2. Deletion of 42 aa in the Lsm-AD in ataxin-2 results in cytotoxicity without significant abnormalities in the Golgi apparatus. These findings suggest that the C-terminal domains are important for ataxin-2 cytotoxicity and that Golgi abnormalities may not be primary in the pathogenic process.