Gastrointestinal stromal tumors (GISTs) have been a topic of increasing interest since the discovery of their cellular activation pathway via the receptor for tyrosine kinase (KIT) leading to the possibility of targeted molecular therapy in the form of imatinib mesylate. Endoscopic diagnostic and therapeutic possibilities have also been developing at a rapid pace in recent years. Endoscopic ultrasonography (EUS) allows for an accurate assessment of submucosal tumors and can provide tissue samples for diagnostic purposes using fine needle aspiration techniques. Several newer endoscopic techniques, including contrast enhanced EUS and endoscopic submucosal dissection, have also proven useful in the management of GISTs. Although the many recent studies have focused on the role of endoscopy in diagnosing and treating GISTs, we still need better evidence in order to formulate accurate guidelines.