Spinocerebellar ataxia type 3 (SCA3) is caused by a CAG/polyglutamine repeat expansion in the SCA3 gene. To analyse the pathogenic mechanisms in SCA3, we have generated ataxin-3-expressing rat mesencephalic CSM14.1 cells. In these cells, a post-mitotic neuronal phenotype is induced by temperature shift. The isolated stable cell lines provided high level expression of non-expanded (Q23) or expanded (Q70) human full-length ataxin-3. CSM14.1 cells expressing the expanded full-length ataxin-3 developed nuclear inclusion bodies, strong indentations of the nuclear envelope and cytoplasmic vacuolation. These ultrastructural alterations were present prior to a significantly decreased viability of neuronally differentiated cells expressing expanded ataxin-3. The observed spontaneous cell death did not correlate with formation of intranuclear inclusions and was not apoptotic by ultrastructural analysis. No increased susceptibility to staurosporine-induced apoptosis was found for the expanded or non-expanded ataxin-3-expressing cell lines. These data show that high level expression of expanded full-length ataxin-3 in a neuron-like cell line generates ultrastructural alterations of SCA3 pathogenesis and results in increased spontaneous non-apoptotic cell death.