Abstract: Objective To study the relative risk factors for residual gastrointestinal neuroendocrine tumors at resection margin after endoscopic treatment. Methods One hundred and eighteen patients with gastrointestinal neuroendocrine tumors who underwent endoscopic treatment in our center from February 2002 to July 2012 were included in this study. The clinical data about 22 patients with residual gastrointestinal neuroendocrine tumors at resection margin after endoscopic treatment were retrospectively analyzed. Effects of different parameters on the resection margin was analyzed by univariate analysis. Independent risk factors for the resection margin were analyzed by multivariate logistic regression analysis. Results The 22 patients with residual gastrointestinal neuroendocrine tumors at the resection margin after endoscopic treatment accounted for 18.6% of the 118 patients with gastrointestinal neuroendocrine tumors. Univariate analysis showed that the tumor invasion depth, positive and negative margins, established diagnosis of tumor before endoscopic treatment and the number of years in endoscopy physicians were significantly different between patients with positive resection margin and those with negative resection margin. Multivariate logistic regression analysis showed that the tumor invasion depth was an independent factor for positive resection margin. Conclusion The incidence of positive resection margin is low in patients with residual gastrointestinal neuroendocrine tumors at resection margin after endoscopic treatment if the diagnosis of tumor is established, the tumor invasion is limited to the submucosa, and the operation is performed by senior surgeons.