<b><i>Introduction:</i></b> Ectodermal dysplasias (EDs) are a large group of rare and complex genetic disorders, affecting the development of two or more ectodermal structures. Hypohidrotic ED (HED) is the most frequent ED’s phenotype and is characterized by hypodontia, hypotrichosis, and hypo/anhidrosis, leading to heat intolerance and hyperthermia. <b><i>Case Presentation:</i></b> We report a case of a 2-year-old girl with hair and teeth abnormalities associated with severe digestive symptoms responsible for failure to thrive. Genetic analysis by mass sequencing in parallel on a 4,867-gene panel was performed in duo (index case and her mother). The girl showed the presence of a new de novo c.100dupG variant in <i>EDA</i> responsible for HED associated with a diagnosis of food protein-induced enterocolitis syndrome (FPIES). <b><i>Conclusion:</i></b> We describe a patient with HED and a new <i>EDA</i> variant associated with a diagnosis of FPIES, both implicating increased intestinal permeability. The inclusion of FPIES as a possible digestive symptom of HED can be suggested, although it may occur only in a context of atopy.