Various molecular processes including unfolded protein response, protein transport, synaptic transmission and transcription are implicated in the pathology of polyglutamine diseases caused by the expanded polyglutamine-containing proteins. More than 20 transcription-related factors have been reported to interact with disease proteins, and the pathological interaction is known to repress gene expression. The whole shape of nuclear events evoked by disease proteins is now emerging with information on these transcription-related factors and with findings on the similarity between nuclear bodies and pathological inclusion bodies. This article reviews 'transcription theory', a rapidly growing hypothesis in polyglutamine diseases.