Atopic disorders and gastroesophageal reflux disease (GERD) are some of the most common medical conditions treated by primary care physicians and specialists alike. The observation that atopic disorders, like asthma, allergic rhinitis and sinusitis, food allergies, atopic dermatitis, contact dermatitis, and eosinophilic esophagitis are common comorbidities in patients with GERD raises the question of the nature of the relationship that may exist between GERD and atopic disorders. In this article, we review the pathophysiology of GERD, its effect on the immune system, the effect of acid-blocking medications on allergic responses, as well as several common atopic conditions that have been associated with GERD including asthma, chronic rhinosinusitis (CRS), allergic rhinitis (AR), atopic dermatitis (AD), contact dermatitis (CD), food allergies, proton pump inhibitor (PPI)-responsive esophageal eosinophilia (PPI-REE), and eosinophilic esophagitis (EoE). In each condition, the evidence of a causal link is not definitive. Although the relationship between asthma and GERD remains controversial, evidence suggests that a subset of asthma patients with documented GERD may experience improved asthma control following appropriate treatment of GERD. The relationship of GERD to allergic rhinitis and chronic sinusitis is weak; however, studies support the concept that treatment of frequent episodes of GERD can have a positive effect on rhinitis and sinusitis overall. The relationship between allergic sensitization and GERD is likely bidirectional. GERD may induce changes in the mucosal immune system that may favor the development of food allergy and allergic sensitization to aeroallergens; however, the underlying mechanisms have not been established.