Heat Shock Protein (Hsp90) is a pro‐survival molecular chaperone essential for the proper folding of a wide range of cellular proteins. It is highly abundant in most cell types and exists as a dimer that interacts with the client proteins. It is well described that the activity of Hsp90 is regulated by post‐translational modifications. We showed that in pathological conditions in which the powerful oxidant peroxynitrite is produced, Hsp90 undergoes nitration at 5 out of 24 tyrosine residues (Y) in its sequence. Further, nitration at Y33 and/or Y56 induces a pathological gain‐of‐function in Hsp90, leading to decreased mitochondrial activity and activation of the purinergic P2X7 receptor, which in motor neurons induces cell death. This is the first nitrated protein with a pathological function described to date. Nitration of Hsp90 is of particular relevance in amyotrophic lateral sclerosis (ALS), a motor neuron degenerative condition with an elusive pathogenesis and scant treatment options. We discovered that Hsp90 is endogenously nitrated in motor neurons in the spinal cord of ALS patients, the cell type that is compromised in this disease process. Establishing the structural changes induced in Hsp90 by nitration that lead to the pathological toxic function is crucial for the development of novel therapeutic strategies for ALS treatment. Here, using a combination of biophysical approaches we show that nitration of Hsp90 at Y33 and Y56, the residues relevant to the toxic function, had a profound impact on Hsp90 structure. To dissect the contribution of nitration at Y33 and/or Y56 on Hsp90 structural changes, we performed analytical ultracentrifugation sedimentation velocity experiments using recombinant Hsp90, peroxynitrite‐treated Hsp90 (fully oxidized protein), and site‐specific nitrated Hsp90 produced by genetic code expansion, carrying nitrotyrosine at either position 33 or 56, or simultaneously at both positions as the sole modification in the protein. Following peroxynitrite treatment, Hsp90 dimer was destabilized, showing a significant increase in the number of monomers, and the formation of oligomeric species. These results were confirmed by negative stain cryo‐electron microscopy, and size exclusion chromatography followed by multiangle light scattering. Site‐specific nitration at Y33 or Y56 was enough to destabilize the dimer conformation, while simultaneous nitration at Y33 and Y56 most closely resembled the structural changes observed after peroxynitrite treatment. In contrast, replacement of Y33 and Y56 by nitration‐resistant phenylalanine decreased dimer destabilization and prevented oligomer formation after peroxynitrite treatment. Together, these results suggest that nitration at Y33 and Y56 is enough to significantly affect the global structure of Hsp90, and that these changes may be responsible for nitrated Hsp90's toxic gain‐of‐function. Thus, targeting these structural changes may lead to the development of drugs that selectively inhibit nitrated Hsp90's pathological activity in ALS, without affecting the function of the unmodified chaperone in normal tissues.