Subepithelial lesions are increasingly being identified with improved endoscopic imaging technologies. Many of these lesions are now recognized as gastrointestinal stromal tumors (GISTs). Recent advances in immunohistochemistry have allowed for reliable differentiation of GISTs from other subepithelial tumors, thereby significantly improving our understanding of these lesions. The wealth of recent information and continual evolution in our understanding of GISTs has exposed some knowledge gaps pertaining to the optimal management of these lesions. In this article, we review the endoscopic management of GISTs as it relates to the identification, diagnosis and management of these lesions based on the best available literature and our own clinical experience to date.