Mutations in the myosin 5β, syntaxin-binding protein 2, and syntaxin 3 genes lead to microvillus inclusion disease (MVID), an autosomal recessive congenital enteropathy. This rare disease is characterized by lack of microvilli on the surface of enterocytes in the small intestine, the presence of pathognomonic intracellular microvillus inclusions, and vesicular bodies within these enterocytes. This pathology leads to the characteristic intractable, life-threatening, watery diarrhea. In the more common early-onset form, affected patients present in the first few days after birth, whereas in the late-onset form, clinical manifestations appear at approximately 2 to 3 months of age. Genetic testing can confirm the diagnosis, but the infant’s medical history, clinical presentation, and small intestinal biopsy results are strongly suggestive of the diagnosis. The prevalence of MVID is thought to be higher in countries with a high degree of consanguinity. Patients with MVID cannot tolerate feedings and require continuous total parenteral nutrition. Mortality is extremely high in the early-onset type with reports of survival in patients treated with small intestinal transplantation. Medical counseling for parents of infants with MVID needs to reflect our current understanding of the various genetic forms of this disease, the feasible management, and anticipated outcomes.