Difficulties in early and accurate diagnosis of intestinal tuberculosis lead to frequent misdiagnosis even in endemic areas. This study aimed to investigate clinical and laboratory characteristics of patients with lower gastrointestinal tract tuberculosis (LGITB). Patients who met the criteria for LGITB in a medical center from 1997 to 2006 were identified and their medical records reviewed. A number of 4,567 patients with culture or histology-proven tuberculosis were identified, and 30 (0.66%) were diagnosed with LGITB. Principal co-morbidities were type II diabetes mellitus (23%) and alcoholism (23%). Twenty-two (73%) had radiographic findings suggestive of pulmonary tuberculosis, which was culture-proven in 13. Mycobacterial cultures from stool or sputum had diagnostic yields of about 50%, comparable to that of histological studies of colonoscopic or surgical biopsies. Multidrug-resistant tuberculosis (MDRTB) was identified in four patients, including two alcoholics. Fourteen underwent surgery; two (14%) received right hemicolectomy under the diagnosis of colon cancer without pre- or intraoperative histological study. The 1-year mortality was 20% but was 50% in patients with MDRTB. A high rate of alcoholism and diabetes mellitus and a high percentage of MDRTB among alcoholics were observed in our patients with LGITB. The diagnostic yields of stool or sputum mycobacterial culture (50%) were similar to that of intestinal histological study. Pre- or intraoperative histological examination could prevent unnecessarily extensive surgery.