Patients with gastroesophageal reflux disease (GERD) have a coexisting diagnosis of functional bowel disease (FBD) in approximately 30% of cases. Symptom improvement after surgical therapy for GERD may be less in patients with FBD when compared to patients without this coexisting problem. A retrospective review of patients undergoing Nissen fundoplication between 1996 and 2000 evaluated patients with documented FBD or FBD symptoms to determine operative outcome. Poor postoperative outcome included recurrent heartburn, gas bloat syndrome, dysphagia requiring reoperation or dilation, or delay in resumption of normal diet. Bivariate comparison and multivariate logistic regression evaluated the independent impact of a documented diagnosis of FBD or preoperative symptoms of FBD on outcome. This study examined 155 patients: 32% reported having symptoms of FBD and 10% had a confirmed diagnosis of FBD. Poor postoperative outcomes occurred in 27%. Patients with a documented diagnosis of FBD were significantly more likely to have a poor outcome when compared to patients without symptoms of FBD (53% vs. 23%, P = 0.01). Patients with preoperative symptoms of FBD (but without a documented diagnosis of FBD) also had a higher incidence of poor outcome (5% vs. 23%, P = 0.09). Patients with FBD are at increased risk of poor results after antireflux surgery. Patients with these conditions should be counseled preoperatively regarding the potential for recurrent postoperative symptoms.