Objective Few studies have systematically assessed symptom‐based diagnoses of functional gastrointestinal disorders (FGID) in China. This study aimed to evaluate the positive endoscopic and ultrasonographic findings in patients with symptom‐based FGID. Methods Adult patients with gastrointestinal symptoms but not red flag symptoms who were empirically diagnosed with FGID underwent an upper or lower gastrointestinal endoscopy. An abdominal ultrasonography was also performed to screen for potential organic diseases. Patients’ data were collected and the Rome III questionnaire was used for symptom‐based assessment. Results Positive endoscopic and ultrasonographic findings were detected in 31.8%, 26.2% and 9.9% of patients with esophageal, gastroduodenal and intestinal disorders, respectively. Among patients diagnosed with FGID using the questionnaire, the rates of positive endoscopic and ultrasonographic findings were higher in patients with upper gastrointestinal symptoms than in those with lower gastrointestinal symptoms. Moreover, patients elder than 34.5 years with upper gastrointestinal symptoms and those elder than 47.5 years with lower gastrointestinal symptoms were more likely to have positive endoscopic and ultrasonographic findings. Conclusions The Rome III questionnaire is a valuable diagnostic tool for screening FGID in China. However, the rates of positive endoscopic and ultrasonographic findings vary depending on the location of symptoms. Endoscopy and ultrasonography have irreplaceable value, especially for investigating upper gastrointestinal symptoms.