Polyglutamine (polyQ) expansion causes nine inherited neurodegenerative disorders, including Huntingtons Disease, Spinobulbar Muscular Atrophy, Dentatorubral-Pallidoluysian Atrophy, and Spinocerebellar Ataxias 1, 2, 3, 6, 7, and 17. The common pathological feature of these diseases is the formation of intracellular polyglutamine inclusions or aggregates. Previous studies have focused on the intranuclear inclusions and found that polyQ proteins can affect gene transcription. Recent studies have revealed that polyQ proteins and their inclusions in neuronal processes can impair intracellular transport. Impaired intracellular trafficking, particularly in axons, may lead to neuronal dysfunction and early neuropathology. In this review, we will discuss the ways that polyQ proteins affect intracellular trafficking with an emphasis on the events that lead to neurodegeneration in Huntingtons disease.