We report the case of a malignant, primary, hepatic gastrointestinal stromal tumor (GIST) that was resected from the liver of a 79-year-old woman. To our knowledge, this is the first primary, hepatic GIST on record. The tumor expressed CD117 (c-Kit protein) and vimentin and had the ultrastructural features of GISTs. Sixteen months after partial hepatectomy and resection of the tumor, a hilar lymph node metastasis was found. The metastatic tumor had the same morphologic features as the primary tumor, but in addition it contained numerous multinucleated giant cells. This case shows that GIST can occur as a primary liver tumor, and accordingly, we point out that not all hepatic tumors with a GIST phenotype should be automatically considered to be metastases from a primary gastrointestinal site.