The aim of this study was to determine the endosonographic characteristics of gastrointestinal stromal tumors (GISTs) of the stomach according to histological risk classification. Twenty-four cases of histologically proven c-kit positive GISTs were divided into three groups according to histological risk: low risk (n = 14), intermediate risk (n = 7) and high risk (n = 3). Endoscopic ultrasonography (EUS) features recorded were: size, ulceration, regularity of marginal border, lobulation, shape of tumor, marginal halo, homogeneity, internal echogenic or cystic foci, and the presence of exophytic development. Significant differences were seen in size between the groups studied (P = 0.026). All tumors in the high risk group had mucosal ulceration, which was more commonly seen in the intermediate risk group compared to the low risk group (P = 0.014). All tumors in the high risk group had irregular borders, but only three cases out of 11 in the low risk group had irregular borders (P = 0.039). Thirteen cases in the low risk group and five cases in the intermediate risk group had an oval or round shape; however, only one case in the high risk group showed this (P = 0.043). The optimal size value for prediction of the intermediate and high risk group was 30 mm. Sensitivity and specificity with this value was 80% and 79%, respectively. Large, especially larger than 30 mm, GISTs of the stomach with irregular borders, mucosal ulceration and a non-oval shape on EUS suggest higher risk GISTs of the stomach. These criteria might aid in the clinical management of GISTs of the stomach.