The pathogenesis of Huntington's disease results from polyQ expansions (>36Q) in the Huntingtin (Htt) protein.1 These polyQ expansions make Htt less soluble and promote the formation of misfolded oligomers, fibrils and aggregates in Huntington's disease.2 Efforts to prevent aggregation will greatly benefit from a detailed molecular understanding of the misfolding process. However, htt misfolding has been difficult to study as the protein is tough to handle and examine spectroscopically. Here we developed a novel purification scheme to generate recombinant, clean and monomeric Htt exon1, an aggregation prone fragment of htt that is highly expressed in disease. The misfolding of spin labeled derivatives of Htt exon1 were then monitored by EPR in order to obtain site-specific folding information for residues in different regions of the protein. Our data indicate that residues in the N-terminal N17, the middle polyQ region and the C-terminal, proline rich region all undergo structural changes on different time scales. Moreover, we have also found that the aggregation kinetics and mechanisms of aggregation significantly depend on Q length. Overall, the data indicate distinct phases in which different regions of the molecule undergo conformational changes. Each of these stages may afford the design of different compounds intended at altering the aggregation process.1. Bates, GP.; Harper, PS.; Jones, L., editors. Huntington's Disease. Oxford University Press; Oxford, U.K.: 2002.2. Bates, GP.; Benn, C. The polyglutamine diseases. In: Bates, GP.; Harper, PS.; Jones, L., editors. Huntington's Disease. Oxford University Press; Oxford, U.K.: 2002. p. 429-472.