Objective: Explore the relationship between food hypersensitivity associated with cows milk protein allergy (CMPA) and common gastrointestinal and upper aerodigestive disorders found in children less than two years of age. Method: Two-year retrospective chart review of a common cohort of children less than 2 years of age, managed in both a tertiary pediatric gastroenterology and otolaryngology clinic. Comparison with a control pediatric population was performed. Results: Of 191 children reviewed with CMPA, 141 demonstrated upper gastrointestinal (GI) complaints. Twenty-five (18%) of these children had otolaryngologic (ENT) conditions refractory to standard therapy with the majority being chronic otitis media (70%) and oropharyngeal dysphagia (80%). In contrast, only 2% of patients in a GI control group demonstrated ENT disease. Dairy elimination improved GI symptoms in 92 patients, and ENT disease improved in 60%. ENT conditions improved in the control group via standard therapy. Conclusion: This study suggests a relationship between CMPA and ENT concerns in children less than 2 years old, whereby food hypersensitivity can be associated with recalcitrant otits media and oropharyngeal dysphagia. Elimination diets can improve both GI and ENT conditions refractory to GERD therapy in patients with CMPA.