〔Abstract〕 Objective To investigate the clinicopathological features and prognostic factors of small gastrointestinal stromal tumor(GIST). Methods Clinicopathological and mutations features of 34 mini-GIST and 16 micro-GIST patients were retrospectively analyzed. All data were compared with 58 cases of clinically overt GIST with tumor diameter between 2 cm and 5 cm. Results Both the mini-GIST and micro-GIST were predominantly located in the stomach, followed by small intestine and colorectal. The most common pathomorphology of mini-GIST and micro-GIST were spindle cell, mixed cell while epithelioid cell were relatively rare. The mutation rate of KIT in mini-GIST and micro-GIST was lower than that in clinically overt GIST, while the percentage of wild type GIST was significantly higher than that in clinically overt GIST(P<0.05). The mitotic rate, tumor risk grade and Ki67 proliferation index of mini-GIST and micro-GIST were obviously lower than those of clinically overt GIST(P<0.05). However, the synchronous occurrence of digestive tract cancer was much more common in mini-GIST and micro-GIST(P<0.05). Conclusion Most mini-GISTs and almost all micro-GISTs exhibit benign biological behavior and have an excellent prognosis. However, there are still a few mini-GISTs with potential malignancy. Early detection and timely intervention of small GIST with potential malignancy can reduce the risk of recurrence and improve the prognosis.