Malignant gastrointestinal stromal tumors (GIST) are rare mesenchymal tumors originating from the wall of the gastrointestinal tract. Their coexistence with other tumors originating from other germ layers is unique. We have reported a case of a 63-year-old GIST patient presenting as an epigastric mass associated with hepatic tumor. Histologically, the mesenteric tumor was composed of spindle cells showing both neural and smooth muscle differentiation. Immunohistochemical examination showed positive staining for CD117, vimentin, S-100, and SMA, while CD34 antigen was negative. The hepatic tumor was diagnosed as hepatocellular carcinoma (HCC). To the best of our knowledge, this is the first case of GIST and HCC coexistence. The rarity of the case, however, should not lead to ignoring such a possibility in differential diagnosis.