Complete curative resection remains the treatment of choice for nonmetastatic gastrointestinal stromal tumors (GISTs). The safety and feasibility of laparoscopy in the treatment of this disease has been shown, however, the long-term oncologic outcomes of this technique remain unclear. An ongoing prospectively maintained database including all laparoscopically resected gastric and small bowel GISTs (n = 116) at Mount Sinai Medical Center from July 1999 to December 2011 was retrospectively analyzed. Recurrence and survival outcomes were calculated using the Kaplan-Meier method and compared with log-rank test. Tumors were of gastric (77.6%) and small bowel (22.4%) origins. Overall mean tumor size was 4.0 cm (±2.7 cm) and R0 resection was achieved in 113 (97.4%) cases. Overall perioperative complication rate was 14.7%, with a reoperative rate of 4.3% at 90 days. When comparing gastric with small bowel GISTs, a more acute presentation requiring emergent resections was noted in patients with small bowel GISTs (p = 008). However tumor size, operative data, and perioperative outcomes were comparable in both groups (p = NS). At a median follow-up of 56.4 months (range 0.1 to 162.4 months), recurrence rate was 7.8% and comparable in both gastric and small bowel GISTs (p = NS). Risk factors for recurrence on univariate analysis were presence of ulceration/necrosis (p < 0.001) and tumor size >5 cm (p = 0.05). Overall 10-year survival rate was 90.8%. Gastric and small bowel overall survival rates were similar (90.7% vs 91.3%, respectively). Overall 10-year disease-free survival was 80.0% (84.3% gastric vs 71.6% small bowel; p = NS). Our series demonstrates the safety and feasibility of laparoscopy in patients undergoing resection of small bowel and gastric GISTs. Comparable long-term oncologic outcomes with a 10-year survival of 90.8% were achieved.