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Abstract Background GISTs are rare tumors but the most frequent mesenchymal tumors of the digestive tract. Diagnosis and treatment are challenging in low-income countries due to relatively poor access to immunohistochemistry and targeted therapy. In Africa, there are few studies about it. Imatinib, an oral targeted therapy, has been available in Benin since 2010 and free since 2016. This study describes the diagnosis and therapeutic management of GIST in Cotonou, Benin. Methods This is a descriptive cross-sectional study, with retrospective data collection over a 10-year period from 2010 to 2020, focused on patients with histological confirmed gastro-intestinal stromal tumor (GIST). Cases were identified using the registry database and the archival files of the Hubert Koutoukou Maga National University Hospital of Cotonou (CNHU-HKM). Results Fifteen GISTs were identified during the study period. The median age was 52 and the sex ratio was 2:1 (10 males and 5 females). The most frequent symptom was abdominal pain (n = 12). Delay in care seeking after onset of symptoms ranged from 24 h to 15 years. The most common site for GISTs was the stomach (n = 8). The median tumor size was 11 cm and the majority (n=10) was metastatic or locally advanced at the time of diagnosis. The tumors were often spindle-shaped at histology (n = 13) and the majority expressed KIT (n = 14). Most of the tumors (n = 12) were at high risk of recurrence according to the Joensuu scoring system. The availability of imatinib has improved the outcome of GIST with response in all cases it was used in neoadjuvant setting (n = 7). Conclusion GISTs are rare tumors and preferentially affect the stomach in Cotonou). Most of the tumors were large, unresectable at the time of diagnosis and at high risk of recurrence. Access to imatinib has revolutionized the management of those tumors in our country.