Gastroesophageal reflux disease (GERD) is a condition characterized by persistent symptoms and complications resulting from reflux of gastric contents into the esophagus. Short-chain fatty acids (SCFAs) are fermentation products of dietary fibres by the gut microbiota and are often studied for their anti-inflammatory and anticancer effects. The presence of SCFAs in the upper gastrointestinal tract, including in patients with GERD, has not been previously studied. The aim of this study was to investigate the relationship between the concentrations of SCFAs in the saliva of different age groups of patients with GERD. The study included 86 patients diagnosed with GERD, divided into two groups according to age: under and over 60 years of age, treated in the Gastroenterology and Hepatology Outpatient Clinic of the University Hospital in Cracow and 39 patients without gastrointestinal tract diseases. After clinical examination, blood was drawn to determine complete blood count, haemoglobin, and CRP. The oral cavity was examined, and unstimulated mixed saliva was collected. The SCFAs analysis was made by liquid chromatography-tandem mass spectrometry after facile derivatization coupled with liquid-liquid extraction. Of the six SCAFs studied, the highest median concentrations of acetic acid and propionic acid were observed in the saliva of patients with GERD and in the control group, in both the younger and older groups of patients. The concentrations of acetic acid and propionic acid were also higher compared with the four other fatty acids in the saliva of patients with GERD and in the control subjects. There were no correlations between salivary SCFAs levels and selected clinical and endoscopic parameters, including chronic inflammatory changes of the esophagus and stomach. In conclusions: SCFAs are present in the saliva of patients with GERD and in the control healthy persons. With the exception of valeric and isovaleric acids, salivary levels of SCFAs were significantly higher in patients with GERD compared to the control group. The highest concentrations of acetic acid and propionic acid were observed in patients with GERD and in both the younger and older patient groups. There were no differences in the concentrations of SCFAs in the saliva of female and male groups. We found no correlations between salivary SCFAs levels and selected clinical, laboratory and endoscopic changes of the oesophagus and stomach.