P/Q-type voltage-gated calcium channels are regulated, in part, through the cytoplasmic carboxyl terminus (C terminus) of their alpha1A subunit. Genetic absence or alteration of the C terminus leads to abnormal channel function and neurological disease. Here we show that the terminal 60-75 kD of the endogenous alpha1A C terminus is cleaved from the full-length protein and is present in cell nuclei. Antiserum to the C terminus (CT-2) labels both wild-type mouse and human Purkinje cell nuclei, but not leaner mouse cerebellum. HEK cells stably expressing beta3 and alpha2delta subunits and transiently transfected with full-length human alpha1A contain a 75 kD CT-2 reactive peptide in their nuclear fraction. Primary granule cells transfected with C-terminally GFP-tagged alpha1A exhibit GFP nuclear labeling. Nuclear translocation depends partly on the presence of three nuclear localization signals within the C terminus. The C-terminal fragment bears a polyglutamine tract which, when expanded (Q33) as in spinocerebellar ataxia type 6 (SCA6), is toxic to cells. Moreover, polyglutamine-mediated toxicity is dependent on nuclear localization. Finally, in the absence of flanking sequence the Q33 expansion alone does not kill cells. These results suggest a novel processing of the P/Q-type calcium channel and a potential mechanism for the pathogenesis of SCA6.