Although expansion of a polyglutamine tract in the huntingtin protein is known to cause Huntington's disease (HD), there is considerable debate as to how this mutation leads to the selective neuronal loss that characterizes the disease. The observation that mutant huntingtin accumulates in neuronal nuclei has led to the hypothesis that the molecular mechanism may involve the disruption of specific nuclear activities. Recently, several nuclear interaction partners for huntingtin have been identified, including HypA, a splicing factor-like protein of unknown function. Using a yeast two-hybrid screen, we have identified the interaction of HypA with the nuclear scaffold protein NAKAP. Interaction of NAKAP with HypA is specific and occurs both in yeast and in vitro. Deletion-mapping studies indicate that binding occurs via a proline-rich domain in NAKAP with a WW domain of HypA. In cultured cells, NAKAP and HypA localize within the nucleus and copurify with the nuclear matrix. Furthermore, NAKAP associates with HypA from human brain and copurifies with huntingtin protein in brain tissue obtained from HD patients. In HD neurons, NAKAP and mutant huntingtin were colocalized to the nuclear matrix and were found to be components of nuclear aggregates. Hence, the NAKAP-HypA scaffold is a potential nuclear docking site for huntingtin protein and may contribute to the nuclear accumulation of huntingtin observed in HD.