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Objective To evaluate the clinical value of alarm symptoms in diagnosis of lower gastrointestinal diseases. Methods Data of consecutive autochthonous patients referred to the endoscopy center of Renji Hospital during the period of Oct. 2002 to Dec. 2003 were retrospectively analyzed. The prevalence of alarm symptoms in Shanghai patients with colorectal malignancies or other organic or functional lower gastrointestinal diseases was investigated. Results 83 (4. 9% ) cases of colorectal malignancies were found in 1681 patients referred to the center for colonoscopy because of lower gastrointestinal symptoms. All these malignancies were verified to be in the progressive stage. The prevalence of alarm symptoms was 81.9% (68/83). Hematochezia ( OR 4. 1, 95% CI 3.3-5.2, P＜0.001) , melena (OR6.4, 95%CI3.7-11.0, P＜0.001) and anemia (OR9.6, 95%CI3. 7-25. 0, P＜0.001 ) were the most common and specific alarm symptoms. All the patients without alarm symptoms were above the age of 40 years. 264 (15.7%) cases of organic colorectal diseases other than malignancies and 1334 (79.4%) cases with no causal pathology identified were found in 1681 patients, and the prevalence of alarm symptoms in these two groups was 48. 5% (128/264) and 14. 8% (197/1334), respectively. Conclusion Alarm symptoms including hematochezia, melena, and anemia were useful in distinguishing organic from functional colorectal diseases in patients over 40 years old at the onset of symptoms. Furthermore, hematochezia, melena, anemia,severe weight loss, and abdominal mass were helpful in differentiating malignant from non-malignant colorectal diseases. Colonoscopy should be recommended for patients regardless of age with these alarm symptoms, and so do patients above the age of 40 years with no alarm symptoms before the diagnosis of functional diseases are made.