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RATIONALE: Food protein-induced allergic proctocolitis (FPIAP) is an early, common, and burdensome manifestation of food allergy. Yet, its epidemiology, pathophysiology and relationship to other food allergic manifestations remain poorly understood. METHODS: The Gastrointestinal Microbiome and Allergic Proctocolitis (GMAP) Study is an ongoing prospective observational infant cohort which enrolled 1003 healthy newborn infants at their first well visit at a single primary care practice in suburban Massachusetts and followed them for a median of 24 [2, 45] months. Clinical diagnosis of FPIAP including documented blood in stool was made by expert clinicians. RESULTS: 903 infants were analyzed (46% female, 89% term, 32% delivered via caesarian section, 9% neonatal antibiotics). 153 cases of FPIAP were identified, giving a cumulative incidence of FPIAP in this unselected population of 17% over three years. Infants fed both breastmilk and formula at any point during the first 4 months were 56% less likely than infants fed exclusively formula and 38% less likely than infants fed exclusively breastmilk to develop FPIAP (HR 0.44, p50.005; HR 0.62, p<0.050). Eczema (OR 1.5 [1.1, 2.2], p50.021) and family history of food allergies (OR 1.9 [1.2, 2.8], p50.005) were among risk factors for FPIAP development, while caesarian section, antibiotic exposure, and siblings were not. Infants fed exclusively formula developed FPIAP at a significantly younger age than those exposed to breastmilk (15.6 vs. 32.4 days, p<0.001). CONCLUSIONS: The prospectively defined incidence of FPIAP is strikingly higher than published estimates. Infants fed both formula and breastmilk appeared most protected against FPIAP development.