BACKGROUND: Eating disorders (EDs) are serious psychiatric disorders with an estimated 3.3 million healthy life-years lost worldwide yearly. Understanding the course of illness, diagnostic transitions and remission, and their associated genetic correlates could inform both ED etiology and treatment. We investigated occurrences of ED transitions and presumed remission and their genetic correlates as captured by polygenic scores (PGSs) in a large Danish register-based cohort. METHODS: The sample comprised 10,565 individuals with a diagnosis of anorexia nervosa (AN), bulimia nervosa (BN), or eating disorder not otherwise specified (EDNOS) and with at least two registered hospital contacts between 1995 and 2018. Based on medical records, the occurrence of diagnostic transitions and periods of presumed remission were identified. Associations between 422 PGSs and diagnostic transitions and presumed remission were evaluated using Cox proportional hazard models. RESULTS: A minority of ED cases (14.1%-23.1%) experienced a diagnostic transition. Rates of presumed remission ranged between 86.9% and 89.8%. Higher (1 SD increase) PGSs for major depressive disorder and multisite chronic pain were positively associated with transitioning from AN to either BN or EDNOS. Higher PGSs for a measure of body fat percentage and financial difficulties were positively associated with presumed remission from AN. Having a higher PGS for mood swings was positively associated with presumed remission from EDNOS whereas higher PGS for overall health rating showed the opposite. CONCLUSIONS: We found that most patients with an ED did not experience diagnostic transitions but were more likely to experience a period of presumed remission. Both diagnostic transitions and presumed remission have a significant polygenic component.