Heterotopic gastric mucosa in the upper esophagus (HGMUE) is reported to be related to gastroesophageal reflux disease (GERD). This study investigated the prevalence of GERD and the use of salivary pepsin to diagnose gastroesophageal reflux, especially proximal reflux, in HGMUE patients. One hundred and fifty-three HGMUE patients and 50 healthy volunteers were studied. All subjects took a reflux symptom index questionnaire (RSI); underwent endoscopy, barium esophagogram, high-resolution manometry (HRM), and 24-hour multichannel intraluminal impedance-pH-metry (MII-pH); and salivary pepsin test. Ninety-five (62.1%) HGMUE patients but no control subjects were diagnosed with GERD. The salivary pepsin concentration, RSI score, DeMeester score, acid exposure time (AET), total reflux episodes, proximal acidic reflux episodes, and proximal weakly acidic reflux episodes were significantly higher in the HGMUE group than in the control group (P < 0.05). The salivary pepsin test showed a sensitivity of 85.9% and specificity of 56.9% for diagnosing GERD using the optimal cut-off value of 75ng/mL. One hundred and seven (69.9%) and 46 (30.1%) HGMUE patients were categorized as pepsin (+) and pepsin (-), respectively when 75ng/mL was used as a cut-off value. Male sex, RSI, AET, and proximal acid reflux episodes were positive predictive factors for the occurrence of pepsin (+) in HGMUE patients. GERD, especially GERD with proximal acid reflux and related symptoms, was common in HGMUE patients. The salivary pepsin test could be an additional useful test for testing reflux in HGMUE patients, but it will not replace the MII-pH.