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Gastrointestinal stromal tumors (GIST) are the most common type of mesenchymal malignancies of the gastrointestinal (GI) tract. Almost 10% of them are originated outside of the GI tract (extra-GIST), while GIST of the greater omentum constitutes about 1% among stromal tumors. More than 80% of GIST have mutations in c-KIT and PDGFRA genes. Herein we demonstrate the case of successful treatment of patient with giant omental GIST with c-KIT exon 11 mutation. 64-years-old woman, was admitted to the Department of abdominal oncology with complaints of shortness of breath and abdominal enlargement in volume. CT-scan revealed a large tumor in the abdominal cavity with tumor size of 54×34×22 cm. The patient underwent left thoraco-abdominal approach. It was found that the tumor was originated from the greater omentum with several metastases located on the peritoneum of the left lateral channel. Resection of the large omentum, splenectomy, liver resection and was done. Postoperative immunohistochemical study showed the expression of CD117, CD34 in tumor cells. Ki-67 index was 12–15%. Genetic study revealed c-KIT exon 11 mutation. Treatment with imatinib 400 mg per day was started. Patient has been treated with imatinib for 12 years. On control examination we have found a metastasis in the anterior abdominal wall 3,5×3×2,5 cm in diameter. Afterwards we performed resection of anterior abdominal wall with metastasis on 9 November 2017. Immunohistochemical study confirmed metastasis of GIST. The index of tumor proliferation activity (Ki-67) was 45%. Patient prolonged imatinib treatment at the dose of 400 mg per day after operation. No signs of progression have been revealed on control examination 72 months after the operation. 12-year progression-free survival during imatinib treatment is unique in our practice. Moreover, in the case of further progression, we have second and third-line targeted therapy (sunitinib and regorafenib) and surgery treatment in local progression.