Background: Low birth prevalence and referral bias constitute significant obstacles to elucidating the natural history of Ebstein anomaly (EA). Objectives: An extensive 2-country register-based collaboration was performed to investigate the mortality in patients with EA. Methods: Patients born from 1970 to 2017 and diagnosed with EA were identified in Danish and Swedish nationwide medical registries. Each patient was matched by birth year and sex with 10 control subjects from the general population. Cumulative mortality and HR of mortality were computed using Kaplan-Meier failure function and Cox proportional regression model. Results: The study included 530 patients with EA and 5,300 matched control subjects with a median follow-up of 11 years. In the EA cohort, 43% (228) underwent cardiac surgery. Cumulative mortality was lower for patients diagnosed in the modern era (the year 2000 and later) than for those diagnosed in the prior era (P < 0.001). Patients with isolated lesion displayed lower cumulative mortality than patients with complex lesions did (P < 0.001). Patients with a presumed mild EA anatomy displayed a 35-year cumulative mortality of 11% (vs 4% for the matched control subjects; P < 0.001), yielding an HR for mortality of 6.0 (95% CI: 2.7-13.6), whereas patients with presumed severe EA demonstrated an HR of 36.2 (95% CI: 15.5-84.4) compared with control subjects and a cumulative mortality of 18% 35 years following diagnosis. Conclusions: Mortality in patients with EA is high irrespective of presence of concomitant congenital cardiac malformations and time of diagnosis compared with the general population, but overall mortality has improved in the contemporary era.