ARD1 (arrest-defective protein 1), together with NAT1 (N-acetyltransferase protein 1), is part of the major N(alpha)-acetyltransferase complex in eukaryotes responsible for alpha-acetylation of proteins and peptides. Protein acetylation has been implicated in gene expression regulation and protein-protein interaction. We characterized the native folded and misfolded conformation of hARD1. Structural characterization of native hARD1 using size exclusion chromatography, circular dichroism, and fluorescence spectroscopy shows the protein consists of a compact globular region comprising two thirds of the protein and a flexible unstructured C terminus. In addition, hARD1 forms protofilaments under physiological conditions of pH and temperature, as judged by electron microscopy and staining with the dyes Congo red and thioflavin T. The process is accelerated by thermal denaturation and high protein concentrations. Limited proteolysis of aggregated hARD1 revealed a resistant fragment whose sequence matched a region contained within the acetyl transferase domain.