Gastrointestinal stromal tumor (GIST) is the most common mesenchymal tumor of the gastrointestinal tract. Tyrosine kinase inhibitors (TKIs), such as imatinibmesylate, have been used for the adjuvant treatment of KIT-positive GISTs. Several pathologic changes after imatinib treatment of metastatic GIST including tumor necrosis, myxohyaline or sclerohyalinestroma, proliferative index decline, a varying degree of hemorrhage, edema, and cystic change have been reported in previous studies. More specifically, cystic changes after imatinib treatment were mainly induced by necrosis, hemorrhage, and degeneration. Until now, there have been no reports of cystic changes due to a dilated bile duct entrapped by a totally regressed tumor. We report a case of a 61-year-old man who was diagnosed with high-risk GIST of the stomach complicated by hepatic metastasis and who had such a unique pathologic changes with imatinib treatment.