Abstract: AIM:To evaluate the efficacy and safety of septal ablation and myectomy in treatment of hypertrophic cardiomyopathy. METHODS: PubMed, MedLine, Cochrane library and China National Knowledge Infrastructure (CNKI) databases were searched for literature on clinical trials of septal ablation in treatment of hypertrophic cardiomyopathy in comparison with myectomy, using key words “hypertrophic cardiomyopathy,” “septal ablation” and “myectomy.” A manual search of those trials was simultaneously performed. A meta-analysis was conducted on the outcomes of the included trials with the assistance of RevMan 5.025 software. RESULTS: A total of seven randomized controlled trials (RCT) were discovered including 445 patients. No significant difference was found in the all-cause mortality (RD=0.00, 95%CI:-0.03 to 0.04, P=0.88) and reduction in left ventricular outflow tract gradient (4.50, 95%CI:-1.08 to 10.07, P=0.11) between septal myectomy group and septal ablation group. The post-procedure ventricular arrhythmia rate, pacemaker implantation rate (OR=1.67, 95%CI: 0.86 to 3.26, P=0.13) and mitral regurgitation rate revealed insignificant differences. But the post-procedure reduction in NYHA functional class in septal ablation group was lower compared with that in the septal myectomy group (0.31, 95% CI: 0.16 to 0.45, P<0.01). CONCLUSION: There is no significant difference in efficacy and safety between septal ablation and myectomy in treatment of hypertrophic cardiomyopathy. Septal ablation is less effective for improvement of cardiac functions.