Background: Autonomy describes a psychological state of self-regulation of motivation and action, which is a central characteristic of healthy functioning. In neurodegenerative diseases measures of self-perception have been found to be affected by the disease. However, it has never been investigated whether measures of self-perception, like autonomy, is affected in Huntington's disease. Objective: We investigated whether autonomy is affected in Huntington's disease and if the degree of autonomy is associated with motor function, neuropsychiatric symptoms, cognitive impairments, and apathy. Methods: We included 44 premanifest and motor-manifest Huntington's disease gene expansion carriers and 19 controls. Autonomy was examined using two self-report questionnaires, the Autonomy-Connectedness Scale-30 and the Index of Autonomous Functioning. All participants were examined according to motor function, cognitive impairments, and neuropsychiatric symptoms, including apathy. Results: Statistically significant differences were found between motor-manifest Huntington's disease gene expansion carriers and premanifest Huntington's disease gene expansion carriers or controls on two measures of autonomy. Between 25-38% of motor-manifest Huntington's disease gene expansion carriers scored significantly below the normal level on subscales of autonomy as compared to controls. One autonomy subscale was associated with apathy (r = -0.65), but not with other symptoms of Huntington's disease. Conclusion: This study provides evidence for impaired autonomy in individuals with Huntington's disease and an association between autonomy and apathy. The results underline the importance of maintaining patient autonomy and involvement in care throughout the disease.