The aberrant misfolding and subsequent conversion of monomeric protein into amyloid aggregates characterizes many neurodegenerative disorders, including Parkinson’s and Alzheimer’s diseases. These aggregates are highly heterogeneous in structure, generally of low abundance, and typically smaller than the diffraction limit of light (~250 nm). To overcome these challenges, we have developed a method to characterize protein aggregates at the nanometer scale without the need for a conjugated fluorophore. Using a combination of DNA PAINT and an amyloid specific aptamer, we demonstrate that this technique is able to detect and super-resolve a range of aggregated species, including those formed by α-synuclein and amyloid-β. Additionally, this method enables endogenous protein aggregates within cells to be characterized. We found that neuronal cells derived from patients with Parkinson’s disease contain a larger number of protein aggregates than those from healthy controls.