In polyglutamine (polyQ) degeneration, disease protein that carries an expanded polyQ tract is neurotoxic. Expanded polyQ protein exists in different conformations that display distinct solubility properties. In this study, an inducible transgenic Drosophila model is established to define the pathogenic form of polyQ protein at an early stage of degeneration in vivo. We show that microscopic polyQ aggregates are neither pathogenic nor protective. Further, no toxic effect of sodium dodecyl sulfate (SDS) -soluble polyQ protein is observed in our model. By means of filtration, 2 forms of SDS-insoluble protein species are identified according to their size. Coexpression of an ATPase-defective form of the molecular chaperone Hsc70 (Hsc70-K71S) selectively reduces the abundance of the large SDS-insoluble polyQ species, but such modulation has no modifying effects on degeneration. Notably, we detect a distinct Hsc70-K71S-resistant, small, SDS-insoluble polyQ oligomeric species that is closely correlated with degeneration. Our data highlight the toxic role of SDS-insoluble oligomers in polyQ degeneration in vivo.