BACKGROUND Colonoscopy is essential for the diagnosis of intestinal Behcet's disease (BD), which is characterized by a typical oval-shaped ulcer in the ileocecal region. However, potential risks of colonoscopy have rarely been reported. METHODS Herein, we describe a patient with intestinal BD who presented with decreased oxygen saturation and shortness of breath during a diagnostic colonoscopy. Bilateral pneumothorax, pneumomediastinum, pneumoperitoneum, pneumoretroperitoneum and subcutaneous emphysema of the neck, chest, abdomen, back and scrotum were confirmed by computed tomography scan. The sudden change in condition was considered to be associated with iatrogenic bowel perforation. After receiving closed thoracic drainage and conservative therapy, the patient was discharged in stable condition. CONCLUSIONS Endoscopists should be aware of the risks of colonoscopy in patients with intestinal BD and the possibility of pneumothorax associated with intestinal perforation and make adequate preparations before colonoscopy.