We report the association of neurological and intestinal disorders with the reactivation of Epstein-Barr virus (EBV) in a child. This previously healthy 13-yr-old boy presented with pharyngitis and acute abdominal ileus. Laparotomy excluded a mechanical obstruction. Postoperatively, he suffered from prolonged intestinal obstruction, pandysautonomia, and encephalomyelitis. Histological examination of the appendix and a rectal biopsy taken 3 months after the onset showed an absence of ganglion cells (appendix) and hypoganglionosis (rectum), with a mononucleate inflammatory infiltrate in close contact with the myenteric neural plexuses. EBV-PCR was positive in the blood and cerebrospinal fluid, and in situ hybridization with the Epstein-Barr virus encoded RNA probe showed positive cells throughout the appendix wall including the myenteric area, in a mesenteric lymph node, and in the gastric biopsies. EBV spontaneous lymphocytic proliferation was noted in the blood. The serology for EBV showed previous infection but anti-early antigen antibodies were present. No immunodeficiency was found. Neurological and GI recovery occurred after 6 months of parenteral nutrition and bethanechol. The omnipresence of EBV associated with the neurointestinal symptoms suggest that the virus was the causal agent. This is the first documented case of acquired hypoganglionnosis due to EBV reactivation.