Referrals to gastroenterologists or immunologists are common for infants with food allergies that do not involve the immunoglobulin E (IgE) system. Researchers postulated that there might be some diagnostic and treatment differences between these fields for infants with these symptoms. An online computer survey polled the field of pediatric gastroenterology and immunology. There were 3 situations involving infants suspected of having food protein-induced allergic proctocolitis (FPIAP) due to non-IgE-mediated responses to cow’s milk, and the questions focused on diagnosis, treatment, and follow-up. Milk-based formula-fed (case 1) and breastfed (case 2) children with normal appearance and growth were reported, and a breastfed infant who was not growing normally and had a personal and family history of atopy was described in case 3. (case 3). The survey was filled out by 58 pediatric gastroenterologists and 32 immunologists. Recommendations for dietary adjustments in these cases varied widely across gastroenterologists and immunologists. In addition, most doctors affirm the diagnosis based on the disappearance of symptoms following the dietary change, without re-exposure to the potential trigger, even though both organizations developed standards. Further, there was variation in the age at which doctors advocated reintroducing solid foods to infants diagnosed with FPIAP; some said to wait until the child was 12 months old, while others said it could be done as early as 6 months. Despite consensus-based standards, they found that pediatric gastroenterologists and immunologists routinely deviated from them in their diagnosis and treatment of FPIAP. Guidelines for standardizing care should be developed by multidisciplinary task forces, including pediatric primary care providers, gastroenterologists, and immunologists.