This study focuses on endoscopic and pathologic alterations of gastrointestinal (GI) disorders of Iranian patients with common variable immunodeficiency (CVID). Nineteen of 39 CVID patients (48%) had GI complaints. The most common symptom was chronic diarrhea (28%). In endoscopic examination of small intestines, 15 patients had no abnormal finding. Duodenal biopsy revealed villous atrophy in eight and nodular lymphoid hyperplasia in three patients. There was no statistically significant difference between patients with and patients without duodenal villous atrophy regarding the presence of chronic diarrhea, anemia, and absolute CD4+T cells. In three patients, biopsies of the colon showed chronic noncrypt-destructive colitis. GI problems pose a high morbidity to CVID patients and are second only to respiratory complications. CVID patients are at increased risk of infectious and inflammatory conditions in the GI tract. Early diagnosis of these complications improves the quality of life and well-being of patients.