All over the causes of intractable diarrhea of infancy, microvillous inclusion disease is a rare congenital defect of intestinal brush border of unknown aetiology. An autosomal recessive inheritance is suggested by cases occurring in siblings and high incidence of consanguinity. The prognosis of the disease is extremely poor, as life can be sustained only by total parenteral nutrition. The authors report a preterm male newborn of 35 weeks gestation presenting severe hypernatremic dehydration on day 4 after birth caused by a secretory profuse diarrhea and discuss the tools allowing the light microscopic and genetic diagnosis. The final diagnosis of microvillus intestinal disease (MVID) was made on the third month after extensive investigations using electron microscopic examination of intestinal biopsy and genetic confirmation, finding a mutation at the homozygous status of MYO5B gene. The infant died on the fourth month in spite of optimal electrolytic support and parenteral prolonged nutrition. Although MVID is extremely rare, it remains a possible cause of intractable secretory diarrhea leading to severe hypernatremic dehydration and metabolic acidosis in neonates.