A feature of many neurodegenerative diseases is the rearrangement of a specific protein to a non-native conformation, promoting aggregation, amyloid fibril formation, and deposition within tissues or cellular compartments. Such diseases include Alzheimer's disease (AD), Parkinson's disease (PD), and Huntington's disease (HD). Huntington's disease (HD) is caused by an expansion above 35-40 polyglutamine (polyQ) repeats in the huntingtin (htt) protein and results in accumulation of inclusion bodies that contain fibrillar deposits of mutant htt fragments. Intriguingly, polyQ length is directly proportional to the propensity for htt to form fibrils and to the severity of HD, and is inversely correlated to the age of onset. Although the structural basis for htt toxicity is unclear, the formation, abundance and/or persistence of toxic conformers that mediate neuronal dysfunction and degeneration in HD must also be polyQ length-dependent. Here we used atomic force microscopy (AFM) to show that mutant htt fragments and synthetic polyQ peptides form oligomers in a polyQ length-dependent manner. Time-lapse AFM shows oligomers form before fibrils, are transient in nature, and are occasionally direct precursors to fibrils. However, the vast majority of fibrils appear to form by monomer addition that coincides with the disappearance of oligomers. Thus, oligomers must undergo a major structural transition that precedes fibril formation. These results demonstrate that oligomer formation by a mutant htt fragment is strongly polyQ length-dependent, consistent with a causative role for these structures in HD pathogenesis.