Laryngopharyngeal reflux (LPR) is a common defect among laryngological and phoniatric patients. Although LPR is categorized as a superficial gastroesophageal reflux disease (GERD), differential diagnosis should treat these two diseases separately. LPR symptoms can be assessed in the interview using as a tool the reflux symptom index (RSI). In addition, changes in the larynx that occur during LPR might be seen during laryngoscopy and classified according to the reflux finding score (RFS). One of the main mucosal irritants in LPR is pepsin which digests proteins and impairs the functions of the upper respiratory tract cells by affecting carbonate anhydrase (CAIII) and the Sep 70 protein. Pepsin initiates inflammatory changes within the larynx, nasopharynx and nasal cavity. The use of pepsin detection in upper and lower throat secretions is a new direction in LPR diagnostics.