Abstract Background Duodenal GISTs represent 3–5% of all GISTs with limited understanding of patient outcomes. We conducted a retrospective analysis of primary localized duodenal GISTs. Methods Patients were identified via a survey from 16 FSG centers ( n  = 105), and a group of 9 patients enrolled in the BFR14 trial. Data were collected from the original database and patient files, in agreement with French legislation. Results 114 patients were included, with a median age of 57. Tumors originated mainly in D2 (33%), or D3 (24%), with a median size of 5 cm. 109 patients had resection of the primary tumor; with a Local Resection (LR, n  = 82), a pancreaticoduodenectomy (PD, n  = 23), and data were missing for 4 patients. Resections were R0 ( n  = 87, 79%), R1 ( n  = 8, 7%), R2 ( n  = 6). Tumor characteristics were: KIT+ ( n  = 104), CD34+ ( n  = 58). Miettinen risk was low ( n  = 43), and high ( n  = 52). Imatinib was administered preoperatively ( n  = 11) and post-operatively ( n  = 20). With a median follow-up of 36 months (2–250), 98 patients are alive, and 33 relapsed. The 5-year OS and EFS rates are 86.5% and 54.5%. EFS was similar for patients in the LR and the PD groups ( P  >  0.05 ). In multivariate analysis, ECOG PS, and CD34 expression are independent prognostic factors on OS. Miettinen risk and spindle cell type are independent predictive factors for relapse. Conclusions Patients with resected duodenal GIST have a reasonably favorable prognosis. This study favors a preservation of pancreas when there are no anatomical constraints. LR exhibit similar survival and smaller morbidity then PD.