The discovery of KIT gene mutation in gastrointestinal stromal tumor (GIST) has provided a paradigm shift in the classification, diagnosis and molecular-targeted therapy of gastrointestinal mesenchymal tumors. There is growing evidence of phenotype-genotype (KIT, platelet-derived growth factor receptor-alpha, succinate dehydrogenaseor other driver gene mutation) and genotype-therapeutic (sensitivity to imatinib) correlations in GIST. Risk stratification based on mitotic counts, tumor size and rupture is useful for the prognostication and management of patients with GIST. Blood vessel invasion is a strong indicator of liver metastasis in GIST. In addition, novel biomarkers such as cell-cycle regulators, microRNAs and their targets have been discovered by using high throughput molecular analyses. In contrast, leiomyosarcoma of the gastrointestinal tract has become a very rare entity in the ‘KIT’ era, and its molecular pathogenetic mechanism is unclear. Recent studies have revealed a wide spectrum of cytological atypia, mitotic counts and biological behavior of gastrointestinal smooth muscle tumors, suggesting the necessity of establishing the criteria for malignancy. Collectively, both classical histopathological procedures and modern molecular investigations are indispensable for the evolution of diagnosis and treatment of GIST and mimics.