Endoscopy and endoscopic ultrasonography (EUS) are important diagnostic tools for the diagnosis of gastrointestinal stromal tumors (GIST), especially for small incidental GISTs of the stomach and are necessary to make a decision for further procedures. In this overview the technical aspects and the use of endoscopy and EUS in the diagnosis of GIST, including endoscopic probe sampling and resection as well as the current limitations are described. The incidence of GIST and the differential diagnosis by endosonography are also described. This article concentrates on the data based description of the current diagnostic and therapeutic recommendations in suspected small GISTs with respect to the European Society of Medical Oncology (ESMO) guidelines. Finally, the limited options of endoscopic treatment of GIST complications (bleeding, stenosis) and the significance of endoscopy and EUS in further diagnosis of GIST which had been suspected from radiological imaging are briefly discussed.