The giardiasis is a neglected parasitic disease. The WHO has estimated more than 280 million of human infections each year; however, intraepithelial giardiasis is a rare entity, there are only 5 reports showing invasive giardiasis. A pediatric female patient with chronic abdominal pain, diarrhea, or pasty stools, without fever, was seen in the Gastroenterology and Nutrition Service. The stool studies were negative for pathogens and lactose hydrogen breath test was positive. The presumptive clinical diagnosis was giardiasis and the patient was empirically treated with nitazoxanide. But, the patient persisted with abdominal pain and pasty stools. Endoscopy was indicated to search for Helicobacter and Giardia. Guardian and patient gave written informed consent. Hematological profile was normal. The endoscopy was performed under general anesthesia and the biopsies and duodenal aspirate were obtained. The microscopic analyses of duodenal fluid showed Giardia trophozoites. Electron microscopic analysis was negative for Helicobacter pylori, but Giardia trophozoites with a typical crescent shape within the tissue were found. The patient was treated with tinidazole, subsequent tests showed that lactose absorption was normal, stool examinations were negative for Giardia and abdominal pain had stopped. This case suggest that intraepithelial giardiasis could be a common entity but unseen because the giardiasis diagnosis is usually made on fecal samples. Future studies are necessary to determine the role of intraepithelial trophozoites in giardiasis pathogenic mechanisms.