Background Magnetic sphincter augmentation (MSA) is a surgical intervention for gastroesophageal reflux disease (GERD) which has been evaluated in numerous studies and has shown beneficial effects. Long-term effectiveness data for MSA as well as laparoscopic fundoplication (LF) in patients with GERD are needed. Objective The objective of this study was to evaluate the 3-year outcomes for MSA and LF in patients with GERD. Methods This prospective, multi-center, observational registry study evaluated MSA and LF in clinical practice over 3 years (ClinicalTrials.gov identifier: NCT01624506). Data collection included baseline characteristics, reflux symptoms, medication use, satisfaction and complications. Post-surgical evaluations were collected at yearly intervals. Results Between December 2009 and December 2014, 631 patients (465 MSA and 166 LF) were enrolled in the registry. Both MSA and LF resulted in improvements in total GERD-HRQL score (mean reduction in GERD-HRQL from baseline to 3 years post-surgery: MSA 22.0 to 4.6 and LF 23.6 to 4.9) and in satisfaction (GERD-HRQL satisfaction increase from baseline to 3 years: MSA 4.6% to 78.2% and LF 3.7% to 76.5%). Most patients were able to belch as needed with both therapies (MSA 97.6% and LF 91.7% at 3 years). MSA allowed a higher percentage of patients the ability to vomit as needed (MSA 91.2% and LF 68.0% at 3 years). PPI usage declined from baseline to 3 years for both groups after surgery (MSA 97.8% to 24.2% and LF 95.8% to 19.5%). The mean procedure time was shorter for MSA than for LF. Intraoperative and procedure-related complication rates (≤ 2%) were low for both therapies. Conclusions This 3-year prospective observational registry study contributes to the mounting evidence for the effectiveness of MSA and LF. Despite the more severe nature of GERD in the LF group, the clinical outcomes for MSA and LF were favorable from an effectiveness and safety standpoint.