Clinicopathological features and prognosis of omental GISTs are limited due to the extremely rare incidence. Therefore, the aim of the present study was to investigate the clinicopathological features and prognosis of omental GISTs. Omental GISTs cases were obtained from our center and from case reports and clinical studies extracted from MEDLINE. Clinicopathological features and survivals were analyzed. A total of 99 cases of omental GISTs were enrolled in the present study. Omental GISTs occurred predominantly in greater omentum (78/99, 78.8%). The majority of tumors exceeded 10 cm in diameter (67/98, 68.3%) and were high risk (88/96, 91.7%). Histological type was correlated with tumor location and mutational status. The five year DFS and DSS was 86.3% and 80.6%, respectively. Mitotic index was risk factor for prognosis of omental GISTs. Prognosis of omental GISTs was worse than that of gastric GISTs by Kaplan-Meier analysis. However, multivariate analysis showed that the prognosis was comparable between the two groups. The majority of omental GISTs were large and high risk. Mitotic index was risk factor for prognosis of omental GISTs. The prognosis was comparable between omental and gastric GISTs.