Background: Patients with hypertrophic cardiomyopathy (HCM) are generally regarded as having increased risk of arrhythmia, stroke, heart failure, and sudden cardiac death, but reported mortality rates vary considerably and originate from selected populations. Study objective: We aimed to investigate the long-term mortality rate in a nationwide cohort of patients with HCM compared to a matched cohort from the general Danish population. Methods: All patients with a first-time HCM diagnosis in Denmark between January 1, 2007 and December 31, 2018 were identified through nationwide registries. In the main analysis, two visits in an outpatient clinic were required in order to increase specificity. Patients were matched to controls from the background population in a 1:3 ratio based on age, sex, selected comorbidities and date of HCM. Mortalities were compared using Kaplan Meier estimator and multivariable Cox regression models. Results: We identified 3126 patients with a first-time diagnosis of HCM. 1197 patients had at least two visits in the outpatient clinic (43 % female, median age 63.1 [25th–75th percentile 52.1–72.1] years). All-cause mortality was significantly higher in HCM patients than in matched controls: 10-year probabilities of death were 36.4 % (95 % CI 30.2–43.5 %) for HCM patients and 19.4 % (95 % CI 16.8–22.5 %) for controls. After adjusting for additional comorbidities and medications, a diagnosis with HCM was associated with an increased mortality rate (HR 1.48 (95 % CI 1.18–1.84, p = 0.001)). Conclusion: Compared to matched controls from the background population, presence of HCM was associated with a significant increase in mortality rate.