Background: Due to the extremely rare incidence, data of clinicopathological features and prognosis of primary hepatic gastrointestinal stromal tumors (GISTs) is limited. Methods: 36 cases of hepatic GISTs were from the literature, PUBMED, EMBASE, China National Knowledge Infrastructure and WANFANG DATA, and 1 case came from our center. Clinicopathological features and outcomes were analyzed between 37 hepatic GISTs and 254 gastric GISTs from our center. Results: A majority of hepatic GISTs exceeded 5 cm (83.7%), displayed mixed density (69.4%) and spindle morphology (74.2%) and were classified as high risk (91.4%). Larger tumors of hepatic GISTs were likely to display mixed lesion and tumors with mixed lesion were prone to be classified as high risk. In comparisons to gastric GISTs, hepatic GISTs differed from gastric GISTs in tumor size, main symptoms, histologic type, mitotic index, CD34 expression, NIH risk classification. In patients with hepatic GISTs, 5-year DFS and DSS rates were 19.4% and 53.7%, which were worse than that of gastric GISTs (P< 0.001), especially for those with tumor size exceeding 5 cm or mitotic indices exceeding 5/50 HPF (P < 0.001). Multivariable analysis showed location and NIH risk classification were independent prognostic factors for DFS in patients with GISTs, and size and location were significantly associated with DSS. Conclusions: Hepatic GISTs distinguished from gastric GISTs in respect to clinicopathological features and outcomes. Mitotic index exceeding 5/50 HPF or tumor size exceeding 5 cm may be important factor to distinguish hepatic GISTs from gastric GISTs in DFS and DSS.