Gastrointestinal stromal tumor (GIST) is the most common mesenchymal tumor of the gastrointestinal tract. It arises in the stomach, small intestine, colon, rectum and esophagus. KIT gene mutation is a feature of GIST, in addition to PDGFRA gene mutation. KIT gene mutations have been observed to be involved in the development of GIST, its recurrence after surgery and chemotherapy resistance in GIST. Exons 13, 17, 9, and mainly exon 11 are concerned in these biological behaviors of GIST. In this review, we will discuss on the involvement of KIT gene mutations in the tumorigenesis, recurrence and chemotherapeutic resistance of GIST.