Chronic traumatic encephalopathy (CTE) is a neurodegenerative tauopathy that occurs following repetitive traumatic head injury. Electron microscopy revealed the structure of tau filaments sampled from the brains of three sportspeople with CTE to be the same across these individuals but different from tau structures in other tauopathies such as Alzheimer disease. Unlike in other tauopathies, CTE tau filaments formed hydrophobic cavities containing non-proteinaceous molecules, indicating that distinct conformers of assembled tau underlie different neurodegenerative diseases.