AIM: To compare the outcomes between the Stretta procedure and laparoscopic toupet fundoplication (LTF) in patients with gastroesophageal reflux disease (GERD)-related extra-esophageal symptoms. METHODS: From January 2011 to February 2012, a total of 98 patients diagnosed with GERD-related extra-esophageal symptoms who met the inclusion criteria were enrolled in this study. All patients who either underwent the Stretta procedure or LTF treatment have now completed the 3-year follow-up. Primary outcome measures, including frequency and severity of extra-esophageal symptoms, proton pump inhibitor (PPI) use, satisfaction, and postoperative complications, were assessed. The results of the Stretta procedure and LTF therapy were analyzed and compared. RESULTS: There were 47 patients in the Stretta group and 51 patients in the LTF group. Ninety patients were available at the 3-year follow-up. The total of the frequency and severity scores for every symptom improved in both groups (P < 0.05). Improvement in symptom scores of cough, sputum, and wheezing did not achieve statistical significance between the two groups (P > 0.05). However, the score for globus hysterics was different between the Stretta group and the LTF group (4.9 +/- 2.24 vs 3.2 +/- 2.63, P < 0.05). After the Stretta procedure and LTF treatment, 29 and 33 patients in each group achieved PPI therapy independence (61.7% vs 64.7%, P = 0.835). The patients in the LTF group were more satisfied with their quality of life than those in the Stretta procedure group (P < 0.05). Most complications resolved without intervention within two weeks; however, two patients in the LTF group still suffered from severe dysphagia 2 wk after the operation, and it improved after bougie dilation treatment in both patients. CONCLUSION: The Stretta procedure and LTF were both safe and effective for the control of GERD-related extra-esophageal symptoms and the reduction of PPI use.