Alpers disease is a recessive mitochondrial disorder caused by mutations in POLG1 and characterized primarily by progressive neurological and hepatic degeneration. Intestinal dysmotility is a frequent symptom, but it is often overshadowed by other clinical manifestations. The onset and progression of Alpers disease vary; however, most patients die during childhood, often before a specific diagnosis has been established. The gastrointestinal neuromuscular pathology of 4 patients, obtained largely from postmortem specimens, showed distinctive eosinophilic cytoplasmic granules in a subset of enteric ganglia and patchy atrophy of small intestinal muscularis externa. The cytoplasmic inclusions corresponded to abnormal mitochondria, which have been reported previously in another mitochondrial disorder (mitochondrial neurogastrointestinal encephalomyopathy) but not in Alpers disease. Recognition of these distinctive light microscopic findings, in an appropriate clinical setting, should prompt the evaluation of an underlying primary mitochondriopathy.