Gastroesophageal reflux disease (GERD) can cause several upper airway symptoms and alter the physiology of nasopharyngeal mucosa, while upper airway diseases in turn might also exacerbate GERD symptoms. For a long time, asthma was considered a risk factor of GERD in the literature. Asthma and allergic rhinitis (AR) are usually identified as united airway disease according to similar epidemiology and pathophysiology; however, the association between AR and GERD is less elucidated. We aimed to evaluate whether AR would increase the development of GERD. Patients diagnosed as AR were identified from the National Health Insurance Research Database between January 1, 2000 and December 31, 2005 without prior history of gastroesophageal reflux disease. The outcome of interest was new-onset GERD. Cox regression models were applied to calculate the hazard ratio (HR) of GERD. We analyzed the data of 193,810 AR patients aged 18 years or older and being free of AR at baseline. The AR cohort (n = 96,905) had a significantly increased risk of GERD over a non-AR cohort (n = 96905) (adjusted HR (aHR) 1.94; 95% CI = 1.88-1.99, p < 0.001). AR may have stronger correlation with GERD than does asthma, although asthma might increase GERD risk by means of certain pathways shared with AR.