A preterm male neonate was diagnosed as having microvillus inclusion disease based on the characteristics of histological and ultrastructural findings. The peripheral blood sample also revealed MYO5B mutation. He had been on long-term parenteral nutrition. However, a bowel segment was seen in the baby's diaper during hospitalization when he was 5 months old. Serial abdominal ultrasound demonstrated progressive dissection of the bowel wall with detached mucosa in real-time. Small intestinal epithelia were seen on the histology of the detached bowel segment. He died 2 weeks after the episode; postmortem autopsy showed diffuse detachment of mucosa of small bowels without perforation. This is the first report of an infant with microvillus inclusion disease that presented with bowel “dissection”. Weakened adhesion and integrity of intestinal epithelial cells caused by MYO5B mutation was speculated to result in the dissection and detachment of the epithelia of the gastrointestinal tract.