Background: A subset of patients undergoing laparoscopic fundoplication presents with atypical throat symptoms, and the benefit of surgery in these patients is debated. These patients can present with throat symptoms alone or in combination with typical reflux symptoms. We evaluated the clinical outcome in these patients and compared their outcomes with a larger group of patients who did not have throat symptoms before fundoplication. Methods: Outcome data for 893 consecutive patients who underwent a laparoscopic fundoplication from January 2002 to June 2008 were collected prospectively and managed on a database. Ninety-three patients with atypical throat symptoms were identified, and divided into subgroups with (n = 66) and without (n = 27) typical reflux symptoms (heartburn and/or regurgitation), and outcomes were compared with patients (n = 800) who didn't have throat symptoms. Symptoms were assessed with analog symptom scores for heartburn and dysphagia, as well as satisfaction with the surgical outcome. Case records for patients with throat symptoms were also reviewed to obtain more detail about specific throat symptoms and their resolution. Results: Cough was the commonest atypical symptom, followed by sore throat. Heartburn scores improved following surgery in all patient groups. Dysphagia was more common 3 months after surgery in patients without throat symptoms, although there were no differences for dysphagia at later follow-up. Following surgery satisfaction scores were highest in patients with atypical throat symptoms who also had typical reflux symptoms, and the scores were lowest in patients who only had atypical throat symptoms. Nearly twice as many patients who had throat and reflux symptoms reported improvement or resolution of symptoms, compared to patients who only had throat symptoms. Conclusions: Fundoplication achieves a good outcome in patients with atypical throat symptoms who also report typical symptoms of reflux. However, surgeons should be cautious about operating on the subgroup of patients with objective evidence of gastroesophageal reflux who describe throat symptoms but do not report heartburn or regurgitation. In this subgroup, expectations of a good outcome should be minimized.