Behcet's disease (BD) is a multisystemic chronic inflammatory disease. It is characterized by recurrent oral and genital ulcers, uveitis, skin lesions and other manifestations, including neurologic, vascular, joint, and gastrointestinal ulcers of variable severity. Recurrent aphthous ulcer (RAU) represents a very common, but poorly understood, mucosal disorder. If a patient of RAU without any other typical symptoms of BD has gastrointestinal symptoms, it is difficult to distinguish this RAU from true BD with gastrointestinal involvement. Because pathognomonic clinical features and tools are absent, the differential diagnosis of these two diseases relies on the characteristic clinical features and the judgement of an experienced physician. Sixty-five out of a total 960 RAU patients and forty-four of 556 BD patients with gastrointestinal symptoms between January 1996 and December 2003 participated in this study. All were evaluated with esophagogastroduodenoscopy and colonoscopy. Clinical, endoscopic and histopathologic findings were analyzed and ELISA tests were conducted to detect serum levels of ASCA and pANCA. No significant difference was found between the two groups. Differential diagnosis between RAU with gastrointestinal symptoms and BD with gastrointestinal involvement requires further prospective, large-scale study.