Dual-sensor esophageal pH monitoring is routinely used to diagnose GERD. However, the proximal sensor may not be in proximal esophagus in patients with shortened esophagi. Our objective was to determine how often the proximal sensor was misplaced and to determine the effect on pH monitoring. Superior margins of the upper and lower esophageal sphincters (UES and LES) were determined prospectively in consecutive patients. Dual sensors were placed 20 and 5 cm above the LES with a fixed 15-cm spacing pH catheter. Patients were classified into subgroups based on the actual location of the proximal sensor. In 661 patients, the proximal pH sensor was in the hypopharynx in 9% of patients, within the UES in 36%, and in the proximal esophagus in 55%. Spearman's correlation for acid exposure was very good between the dual sensors when the proximal sensor was in the proximal esophagus (R = 0.76) but was poor when the proximal sensor was misplaced in the hypopharynx (R = 0.28). The proximal sensor was misplaced in 45% of patients undergoing dual-sensor esophageal pH monitoring. It is important to locate the UES by manometry before interpreting the proximal esophageal pH data.