We report the case of a boy with neuronal intranuclear inclusion disease in whom the diagnosis was made by examination of a rectal biopsy specimen. Intranuclear inclusions were observed in the Auerbach and Meissner plexuses. In an attempt to understand the physiopathology of this very rare disease, we performed polymerase chain reaction (PCR) and reverse transcriptase-PCR analysis for viral nucleic acids of human immunodeficiency virus type 1 (HIV-1), HIV-2, human cytomegalovirus and measles virus. No viral nucleic acids were detected in the biopsy specimen.