Background Patients with gastroesophageal reflux referred for fundoplication present with different symptom patterns. Previous studies have not analyzed the clinical outcome after fundoplication in patients stratified according to symptom patterns. Methods Five hundred eighteen patients undergoing laparoscopic fundoplication were stratified according to reflux symptom patterns: group 1, regurgitation; group 2, poorly controlled reflux; group 3, regurgitation and poor reflux control (combination of 1 and 2); and group 4, symptoms well controlled but patient does not want to continue taking medication. Clinical outcomes (heartburn control, dysphagia, satisfaction) were assessed prospectively using a standardized questionnaire at early (6 months to 2 years) and late (3-5 years) follow-up intervals. Results Preoperative demographic data for the four groups were similar, except for age and the frequency of esophagitis (patients in group 4 were younger and more likely to have esophagitis). Perioperative morbidity was similar for the four groups. Eighty-seven percent of the overall study group was satisfied at early follow-up and 88% at late follow-up. Early clinical outcomes were similar for all subgroups, except dysphagia scores were higher in early follow-up in groups 1 and 3 (P = 0.001). At late clinical follow-up, there were no significant differences in clinical outcome between any groups. Conclusions At early follow-up (6 months to 2 years), patients who had reported regurgitation as the primary indication for surgery had a less favorable clinical outcome for the side effect dysphagia. However, at later follow-up, the type of preoperative reflux symptoms did not influence the clinical outcome.