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This article investigated the feasibility of laparoscopic surgery in unfavorable site gastric gastrointestinal stromal tumors (GISTs).We identified 214 patients who underwent primary gastric GIST resection at our institution (January 2006–December 2014) from a prospectively collected database. These patients were divided into a Favorable group (140 cases) and an Unfavorable group (74 cases) according to the 2014 version of the National Comprehensive Cancer Network Clinical Guidelines (NCCN guidelines).The wedge resection rate of the Favorable group was higher than that of the Unfavorable group, and most procedures were performed laparoscopically (P < 0.05). In addition, there were no differences in the other clinicopathological features between these groups (P > 0.05). The postoperative stay of the Unfavorable group was longer than that of the Favorable group (P = 0.02). Laparoscopic surgery in both groups resulted in a shorter operative time, lower blood loss, faster time to first flatus, faster time to first fluid diet, and shorter postoperative stay than open surgery (P < 0.05). Although the difference was not significant (P = 0.09), the postoperative complication incidence of the Favorable group was less than that of the Unfavorable group (10% vs 17.6%). Furthermore, in the Unfavorable group, the incidence of postoperative complications from laparoscopic surgery was significantly lower than that of open surgery (P = 0.001). There were no differences in the 5-year overall survival (OS) and recurrence-free survival (RFS) of these groups (P > 0.05). Furthermore, in the Unfavorable group, the 5-year OS and RFS were similar for both laparoscopic and open procedures. Multivariate Cox regression analysis showed that imatinib (IM) treatment was an independent risk factor for poor prognosis.Laparoscopic operation for gastric GISTs located in unfavorable sites can yield similar long-term outcomes compared with an open operation. However, laparoscopic surgery has the obvious advantage of being minimally invasive, and the incidence of postoperative complications was low. Laparoscopic surgery is thus an option for the treatment of localized gastric GISTs.