A small percentage of patients who carry the diagnosis of refractory gastroesophageal reflux disease (GERD) actually have eosinophilic esophagitis (EoE). The purpose of this study was to describe a series of patients who underwent fundoplication for presumed refractory GERD, but subsequently were found to have EoE. We performed a retrospective analysis of our EoE database. Patients diagnosed with EoE after Nissen were identified. Cases were defined according to recent consensus guidelines. Five patients underwent anti-reflux surgery for refractory GERD, but were subsequently diagnosed with EoE. None had esophageal biopsies prior to surgery, and in all subjects, symptoms persisted afterward, with no evidence of wrap failure. The diagnosis of EoE was typically delayed (range: 3-14 years), and when made, there were high levels of esophageal eosinophilia (range: 30-170 eos/hpf). A proportion of patients undergoing fundoplication for incomplete resolution of GERD symptoms will be undiagnosed cases of EoE. Given the rising prevalence of EoE, we recommend obtaining proximal and distal esophageal biopsies in such patients prior to performing anti-reflux surgery.