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Objectives: As reported, diagnostic age, gender and presence of outflow tract obstruction have an impact on prognosis in patients with hypertrophic cardiomyopathy. The aim of this study was to compare the long-term outcome between apical hypertrophic cardiomyopathy (ApHCM) and asymmetric septal hypertrophic cardiomyopathy (ASHCM) after the exclusion of these factors. Methods: A total of 540 patients (270 with ApHCM and 270 with ASHCM) identified in a consecutive single-center cohort were retrospectively studied. The two groups were matched by diagnostic age, gender and the presence of outflow tract obstruction. Clinical characteristics and long-term outcomes were compared. Results: The mean follow-up duration in ASHCM and ApHCM were 6.6 ± 5.5 and 7.6 ± 4.1 years, respectively. During follow-up, 16 patients experienced cardiovascular death in the ASHCM group, while 2 patients experienced cardiovascular death in the ApHCM group (6.3 vs. 0.7%, p < 0.01). Cardiovascular morbidity in the ASHCM and ApHCM groups were 39.9 and 18.5% (p < 0.01). In the multivariate Cox regression analysis late gadolinium enhancement (LGE; HR 4.81, 95% CI 1.28-78.0, p = 0.03) and unexplained syncope (HR 9.68, 95% CI 1.9-17.2, p < 0.01) were independent predictors for cardiovascular mortality. Unexplained syncope was independently associated with a higher risk for sudden cardiac death (HR 4.3, 95% CI 1.2-15.3, p = 0.02). Conclusions: After eliminating the interference of diagnostic age, gender and outflow tract obstruction, ASHCM represented a worse prognosis with a higher incidence of cardiovascular mortality and morbidity than ApHCM. LGE was a strong predictor for cardiovascular death.