Gastrointestinal stromal tumors (GISTs) are known to originate specifically from the intestinal cells of Cajal located in the gastrointestinal mesenchyme. GISTs developing outside of the digestive tract have barely been reported. We encountered a first case of large primary GISTs in the liver with cystic changes. A 63-year-old man with a past history of brain infarction visited our hospital. The computed tomography (CT) revealed a 6-cm and a 10-cm mass in the right and the caudal lobe of the liver, respectively. These tumors have marginal enhancement in the arterial phase; however, they presented as hypodense in the internal tumor sites. Both liver tumors had cystic changes. Gastrointestinal examinations using endoscopy revealed no other gastrointestinal tumors, and [18F]-fluoro-2-deoxy-D-glucose positron emission tomography/CT revealed multiple bone metastases in addition to the liver tumors. The liver tumor specimens were composed of spindle cells, and the immunohistochemical staining for c-Kit and for DOG1, as discovered on GIST, was positive. The patient was diagnosed with primary hepatic GIST with cystic changes.