Gastrointestinal stromal tumors are non-epithelial neoplasms that arise from the gastrointestinal tract. Their variable cytologic atypia makes it difficult to predict their prognosis. We report a case of right hepatectomy for a giant metastasis detected 12 years after the surgical treatment of a rectal neoplasm, histologically demonstrated as a low-grade leiomyosarcoma initially, having morphological and immunohistochemical features of low malignancy. Histological examination of the hepatic metastases demonstrated that the tumors were composed of spindle cells similar to those in the rectal neoplasm. Immunohistochemical staining of the hepatic metastases with Ki-67 revealed stronger than the primary tumor. In conclusion, although histological and immunohistochemical analyses provide useful prognostic information, the prognosis of gastrointestinal stromal tumors is difficult to predict. Therefore, a patient with gastrointestinal stromal tumor diagnosed as low-grade malignancy requires carefully long-term follow-up.