Objective Studies have suggested a shared genetic aetiology between congenital long QT syndrome (LQTS) and diabetes, epilepsy and mental disorders. We investigated the prevalence of metabolic, neurological and psychiatric comorbidities in LQTS patients. Methods This retrospective cohort study was based on data from nationwide Danish registries, 2003-2017. LQTS patients were matched 1:5 with controls on sex and age. Results We matched 463 LQTS patients with 2315 controls from the background population. Mean age was 35.7 (SD 21.0) years, and 38% were males in both groups. LQTS patients had a higher prevalence of atrial fibrillation (6.5% vs 2.3%, p<0.001), diabetes (3.7% vs 1.8 %, p=0.011) and hearing loss (3.2% vs 1.7%, p=0.027). LQTS patients had a higher prevalence of psychiatric disorders overall (13.0% vs 9.1%, p=0.01) but the difference could not be attributed to a specific psychiatric disease subgroup. LQTS patients had a higher prevalence of neurological disorders (22.0% vs 13.2%, p<0.001), largely driven by epilepsy (6.7% vs 1.6%, p<0.001). In 20/27 (74%) of the LQTS patients, the epilepsy diagnosis did not reappear in the registries after the LQTS diagnosis was established. Conclusions In this nationwide cohort, patients with LQTS had a significantly increased burden of diabetes, neurological and psychiatric comorbidities, compared with the background population. The higher prevalence of neurological comorbidities was largely driven by epilepsy, despite a high rate of potentially misdiagnosed patients prior to LQTS diagnosis. Our data support that LQTS may be considered a multiorgan disease and suggest that patient management should be adjusted accordingly.