Fungal colonization was observed in the duodenal biopsy specimens of a nine-year-old girl who complained of anorexia and epigastric pain. Endoscopy revealed gastric redness and Geotrichum candidum was identified in the duodenum by histopathology and tissue culture. Immunologic work-up showed low serum levels of IgA and IgM. She was treated with ranitidine and antacids for gastritis. At follow-up, the levels of immunoglobulins had normalized, no fungal elements were detected, and clinical symptoms had disappeared. Duodenal invasion by G. candidum has not been described so far. Duodenal colonization by G. candidum may occur when mucosal immunity is disturbed and may be the source of dissemination in severe immunodeficiency states.