Gastrointestinal stromal tumors(GISTs) are the most common gastrointestinal mesenchymal tumors of the gastrointestinal tract. Most of GISTs are characterized by mutation in the c-kit or PDGFR-α genes. In recent years, detection of gene mutation in GISTs has been widely used. In addition to the contribution to the diagnosis of difficult cases, such detection also has important value in predicting the efficacy of therapeutic drugs targeting, guiding clinical treatment and evaluating the prognosis of patients. In a word, gene mutation detection should be considered as the important standard for exact diagnosis and treatment of GISTs.