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Gastroesophageal reflux disease (GERD) is one of the most commonly encountered disorders in clinical practice nowadays, with an increasing burden on healthcare systems worldwide. GERD-related respiratory symptoms such as unexplained chronic cough, bronchial asthma or chronic obstructive pulmonary disease (COPD) with frequent exacerbations often pose diagnostic and therapeutic challenges and may require a multidisciplinary approach. Moreover, a potential role of GERD as a risk factor has been proposed for chronic rejection in patients who underwent lung transplantation. Pepsin has gained considerable attention from the scientific community in the last few years as a possible surrogate biomarker for GERD. The aim of this narrative review was to provide an overview of the potential utility of pepsin detection as a marker of micro-aspiration in various biological fluids retrieved from patients with suspected GERD-induced respiratory manifestations and in lung transplant patients with allograft dysfunction. Data on the subject remains highly contradictory, and while certain studies support its applicability in investigating atypical GERD manifestations, at the moment, it would be realistic to accept a modest utility at best. A major lack of consensus persists regarding topics such as the optimal timeframe for fluid collection and cut-off values. Further research is warranted in order to address these issues.