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Laparoscopic Heller myotomy (LHM) is the preferred surgical method for treating achalasia. However, peroral endoscopic myotomy (POEM) is providing good short-term results. The objective of this systematic review and meta-analysis was to compare the safety and efficacy of LHM and POEM.A search of PubMed, Cochrane database, Medline, Embase, Science Citation Index, and current contents for English-language articles comparing LHM and POEM between 2007 and 2016 was performed. Variables analyzed included prior endoscopic treatment, prior medical treatment, prior Heller myotomy, operative time, overall complications rate, postoperative gastroesophageal reflux disease (GERD), length of hospital stay, postoperative pain score, and long-term GERD.Seven trials consisting of 483 (LHM=250, POEM=233) patients were analyzed. Preoperative variables, for example, prior endoscopic treatment [odds ratio (OR), 1.32; 95% confidence interval (CI), 0.23-4.61; P=0.96], prior medical treatment [weighted mean difference (WMD), 1.22; 95% CI, 0.52-2.88; P=0.65], and prior Heller myotomy (WMD, 0.47; 95% CI, 0.13-1.67; P=0.25) were comparable. Operative time was 26.28 minutes, nonsignificantly longer for LHM (WMD, 26.28; 95% CI, −11.20 to 63.70; P=0.17). There was a comparable overall complication rate (OR, 1.25; 95% CI, 0.56-2.77; P=0.59), postoperative GERD rate (OR, 1.27; 95% CI, 0.70-2.30; P=0.44), length of hospital stay (WMD, 0.30; 95% CI, −0.24 to 0.85; P=0.28), postoperative pain score (WMD, −0.26; 95% CI, −1.58 to 1.06; P=0.70), and long-term GERD (WMD, 1.06; 95% CI, 0.27-4.1; P=0.08) for both procedures. There was a significantly higher short-term clinical treatment failure rate for LHM (OR, 9.82; 95% CI, 2.06-46.80; P<0.01).POEM compares favorably to LHM for achalasia treatment in short-term perioperative outcomes. However, there was a significantly higher clinical treatment failure rate for LHM on short-term postoperative follow-up. Presently long-term postoperative follow-up data for POEM beyond 1 year are unavailable and eagerly awaited.