Objective To investigate gastroenterologists’ evidence-based medicine (EBM) practice regarding awareness and application and relevant factors as well. Methods Gastroenterologists in hospitals with the level above other districts and counties in Jiangxi province were requested to take part in the survey using questionnaires from December 2010 to February 2011. Results a) Questionnaires were returned by 414 doctors with a response rate of 84.7%, among whom 55.1% respondents were males with the age of 43.2±15.9 years. b) Sixty-four percent respondents were familiar with EBM, which was independently correlated with working experience no less than 10 years (OR=2.32, 95%CI 1.47 to 3.67), from tertiary hospital (OR=1.81, 95%CI 1.12 to 2.93), specialists in gastroenterology (OR=1.74, 95%CI 1.06 to 2.85) and capability of manipulating endoscopy (OR=1.88, 95%CI 1.11 to 3.17). c) Of all the respondents, 53.1% accumulated clinical experience mainly from consensus/guideline, which was independently correlated with the age (OR=2.09, 95%CI 1.83 to 3.24), education level (OR=2.36, 95%CI 1.28 to 4.34) and capability of manipulating endoscopy (OR=2.10, 95%CI 1.29 to 3.42). d) Only 39.4% of doctors mainly depended on EBM to make clinical decision, which was independently correlated with the position (OR=2.38, 95%CI 1.57 to 3.61) and capability of making medical research (OR=1.63, 95%CI 1.05 to 2.55). Conclusion The awareness of EBM in gastroenterologists is fairly good while the practice of medicine is actually influenced by empirical medicine, especially in doctors with younger age, lower education level and lower position.