Sporadic intestinal cryptosporidiosis is not easily diagnosed and might be overlooked. We present here a case of this disease in a 23-year-old Japanese military man with 3 days of abdominal pain, watery diarrhea, and nausea. The frequency of his diarrhea was more than 10 times per day. After his diarrheal bowel symptoms subsided, a colonoscopy was performed because inflammatory bowel disease was suspected. Although the endoscopic findings indicated non-specific ileitis, intestinal cryptosporidiosis was suspected from the histology of ileal biopsy specimens, and this was confirmed ultrastructurally. At that time, however, the patient was on active duty, and thus it was not possible to confirm this as a definitive diagnosis by an adequate stool examination for cryptosporidium. Routine practitioners should be encouraged to carefully inspect patients for this disease, supported by detailed knowledge of it and its diagnosis. If stool-examination results are negative or are not obtained at first, histological diagnosis by endoscopic biopsy could be a useful way to screen for intestinal cryptosporidiosis. Furthermore, stool or histological examination should be performed in recovered patients because the oocysts may continue to be shed for 1 to 4 weeks after the symptoms disappear. Therefore, endoscopic and histological examinations may be useful tools for the early diagnosis of intestinal cryptosporidiosis, although admittedly they are invasive procedures.