Currently, in pediatric practice, a special place is occupied by patients with severe allergic lesions of the gastrointestinal tract, which often manifest immediately after the birth of a child. Food protein-induced enteropathy reduces the quality of life of the child and family; it is difficult to diagnose and to treat. We present a clinical case of a patient with food protein-induced enteropathy, complicated by severe B12-deficiency anemia and edema syndrome. In the tactics of patient management, attention is paid to the late diagnosis of the underlying disease and complications, the complexity of prescribing diet therapy and the lack of alertness regarding the diagnosis of malabsorption associated with food intolerance.