Congenital enteropathies comprise a constellation of rare clinicopathologic diagnoses characterized by intractable watery diarrhea and failure to thrive in infants. These diagnoses include, but are not limited to, tufting enteropathy (TE), microvillous inclusion disease (MID), and enteroendocrine cell dysgenesis (EED). Commonly, the diagnosis is based on identification of their characteristic histologic and/or ultrastructural features in small intestinal mucosa. In cases in which the changes in the small intestine are inconclusive or a small intestine biopsy is not performed, the diagnosis can be hampered or significantly delayed. We describe the histologic features and immunohistochemical staining patterns of gastric and colonic mucosa in patients with confirmed TE (3), MID (2), and EED (1). Specifically, focal epithelial tufts were found in the gastric mucosa of one TE patient and multifocally in the colonic mucosa of another. All TE patients showed complete loss of membranous epithelial EpCAM expression in gastric and colonic mucosa, characteristic of the diagnosis. Gastric biopsies were available in 1 patient with MID; this showed focal disruption of the gastric glandular architecture. Three colon biopsies and 1 resection from 2 patients with MID showed characteristic cytoplasmic vacuoles and periodic acid-Schiff/villin-positive cytoplasmic inclusions. Chromogranin stains showed complete absence of enteroendocrine cells within the colon and a normal distribution in the gastric mucosa of the EED patient. On the basis of our findings, we conclude that the characteristic histologic and immunohistochemical features associated with the small intestine can be confirmed within the gastric and/or colonic mucosa by careful histologic examination and immunohistochemistry.