Aim: Gastro-oesophageal reflux is routinely diagnosed with invasive intraluminal impedance pH probe monitoring. This study aimed to determine whether gastric pepsin A detected in saliva of children correlates with gastro-oesophageal reflux. Methods: Patients undergoing probe monitoring were prospectively recruited between 2014 and 2016 at a paediatric hospital. Standard impedance and demographic data were obtained from electronic medical records. Salivary samples were collected during impedance and measured for gastric pepsin A with an enzyme-linked immunosorbent assay. Impedance probe and pepsin data were analysed and compared for correlation. Results: From 52 enrolled subjects, 28 males and 24 females with mean age 8.0 ± 5.9 and range 0.58-18.0 years, 417 salivary samples were collected. Positive pepsin was found in 14% of samples and 48% patients. The sensitivity of pepsin A in predicting an abnormal impedance was 43% and specificity, 50%. Among pepsin A positive samples, 72% corresponded with a gastro-oesophageal reflux episode. Pepsin peak levels significantly correlated with acidic reflux. Conclusion: Pepsin A was presented in saliva of children undergoing gastro-oesophageal reflux disease investigation. Positive pepsin A was associated with a gastrooesophageal reflux episode, and its peak value correlated with acidic reflux. Salivary pepsin as a marker for gastro-oesophageal reflux needs further investigation.