Gastrin-17 (G-17), pepsinogen-1 (Pg1) and pepsinogen-2 (Pg2) reflect the functional state of gastric mucosa and are used for non-invasive diagnosis and screening of atrophic gastritis. The aim of the study was to clarify if erosive reflux disease (ERD) or non-ERD (NERD) can be distinguished from other dyspeptic conditions in patients, in a non-invasive manner using specific biomarkers. Levels of G-17, Pg1, and Pg2 were measured in 141 ERD patients (median age 48 years, males — 68), 122 NERD patients (median age 45 years, males — 32) and 410 control patients (median age 50 years, males — 97). Levels of biomarkers in ERD and NERD groups were compared to controls. Median levels of G-17 (1.94 vs 2.92 pmol/L, p = 0.036) and Pg2 (6.70 vs 7.79 µg/l, p = 0.046) were lower in the ERD group compared to control patients; no difference with respect to the control was found for the NERD group. After exclusion of the patients having at least one potential condition that might modify the levels of the biomarkers (gastric mucosa atrophy, Helicobacter pylori colonisation), no difference in levels of biomarkers was observed with respect to the control for both the ERD and NERD groups. G-17, Pg1, and Pg2 based tests cannot be used to distinguish ERD or NERD from other dyspeptic conditions in patients.