Abstract Background The gold-standard treatment for esophago-gastric junction outflow obstruction (EGJOO) is still debated. Currently, the management of this motility disorder reflects the experience gained with esophageal achalasia, for which Laparoscopic Heller-Dor (LHD) has been proven to be an effective long-term treatment. However, prospective data comparing long-term results of LHD for these two motility disorders are still lacking. The aim of this prospective, controlled study was to assess the 5-year follow-up of laparoscopic Heller-Dor (LHD) in patients with EGJOO, compared with radiological stage I achalasia patients (ACH). Methods Patients with diagnosis of idiopathic EGJOO, referred for dysphagia or food regurgitation, and radiological stage I achalasia (subgrouped by manometric pattern I, II & III), treated with LHD, were enrolled to the study and then followed prospectively for 5 years. During the follow-up patients were evaluated with Eckard score (ES), Barium-swallow X-ray, High Resolution Manometry (HRM), 24 hour pH-monitoring and Upper-Gastrointestinal endoscopy. The primary outcome was therapeutic success (presence of ES ≤3 or no additional treatment) at the 5-year follow-up assessment. The secondary outcomes included the postoperative IRP and the evidence of gastro-oesophageal reflux. Results The study involved 150 patients: 25 in the EGJOO group and 125 in the ACH group (25 pattern I, 74 pattern II, and 26 pattern III). The patients’ demographic and clinical parameters are summarized in Image. After 5 years, there was no significant difference in success rate: 92% in the EGJOO, 88% in achalasia pattern I, 91.9% in pattern II and 92.3% in pattern III (p=0.95). In the four groups, no differences were shown in the presence of postoperative esophagitis (p=0.08) and in the incidence of abnormal postoperative acid exposure (p=0.87) (Image). Conclusion This is the first long-term comparative study based on prospective data collection to assess the outcome of LHD in patients with EGJOO. After at least 5 years of follow-up, Laparoscopic Heller-Dor has a comparable success rate in both EGJOO and achalasia patients. Based on these data, we conclude that LHD can be proposed as a first-line treatment for symptomatic EGJOO, provided the diagnosis is accurate.