Microvillus inclusion disease (MID) is a congenital disorder with the clinical signs of watery diarrhea often beginning in the first days of life. The main pathological features of the disease include a villus atrophy and an accumulation of periodic acid-Schiff (PAS)-positive material within the apical cytoplasm of enterocytes on the light microscopy level. Electron microscopic criteria are pathognomonic consisting of an increased amount of secretory granules preferentially in crypt epithelial cells and of the presence of microvillus inclusion bodies (MIBs) which are most frequently found in villus enterocytes. Until now the basic molecular defects have not been disclosed completely. In this review we discuss the actual pathogenetic hypothesis and the therapeutic options besides small bowel transplantation.