Purpose of review Gastrointestinal stromal tumors (GIST) are uncommon but important mesenchymal tumors of the GI tract. They are occasionally encountered on routine endoscopy examinations, when identification may present a diagnostic dilemma. The malignant form, fortunately rare, is typically aggressive and resistant to treatment. This paper reviews several important advances over the past several years in the diagnosis and treatment of GIST, as well as in understanding of its pathogenesis. Recent findings Endoscopic ultrasound (EUS) has emerged as the diagnostic measure of choice in the evaluation of submucosal tumors of the GI tract, and EUS criteria have been devised for the identification and characterization of GIST. EUS can also guide needle aspiration of these lesions to obtain diagnostic tissue. The discovery of mutations in a membrane transduction receptor, KIT, has led to greater understanding of the pathogenesis of this tumor and has even provided clues to its cell of origin. Moreover, a unique therapeutic agent, imatinib, has been devised that specifically targets the aberrant KIT receptor and has demonstrated dramatic therapeutic efficacy in this otherwise resistant malignancy. Additional strides have been made in developing consensus definitions for GIST and for their laparoscopic resection. Summary Major advances in GIST diagnosis and treatment have occurred during the past several years and have improved the care of patients with all forms of this tumor.