The objective of the study was to determine the inter-rater variability in assessment of laryngeal findings and whether diagnosing laryngopharyngeal reflux based on the laryngeal findings and history alone without considering allergic rhinitis leads to the overdiagnosis and overtreatment of laryngopharyngeal reflux. Patients with positive and negative skin prick tests were recruited from an allergy clinic in a tertiary teaching university hospital. All subjects completed the Reflux Symptom Index (RSI) and underwent laryngeal examinations by three physicians blinded to the skin prick test results and the Reflux Finding Score (RFS) was determined. RFS >7 or RSI >13 was considered reflux positive. Fleiss' kappa (κ) was used to measure inter-rater agreement. The inter-rater agreement was low for pseudosulcus vocalis (κ = 0.078), ventricular obliteration (κ = 0.206), diffuse laryngeal edema (κ = 0.204), and posterior laryngeal hypertrophy (κ = 0.27), intermediate for laryngeal erythema/hyperemia (κ = 0.42) and vocal fold edema (κ = 0.42), and high for thick endolaryngeal mucus (κ = 0.61). Although the frequency of allergy was high, there was no significant difference between allergy-positive and laryngopharyngeal reflux-positive patients. On logistic regression analysis, thick endolaryngeal mucus was a significant predictor of allergy (p = 0.012, odds ratio 0.264, 95 % confidence interval 0.093-0.74). The laryngeal examination for reflux is subject to marked inter-rater variability and allergic laryngitis was not misdiagnosed as laryngopharyngeal reflux. The presence of thick endolaryngeal mucus should alert physicians to the possibility of allergic rhinitis/laryngitis.