Gastrointestinal stromal tumor (GIST) is the most frequent non-epithelial neoplasm in the gastrointestinal tract. GIST has received much attention both for its clinical significance and biological nature, while the retroperitoneal condition identical to GIST has been rarely described. Presented herein is a case of GIST arising from the retroperitoneum in a 67-year-old man. The solid tumor measuring 4 cm was uncovered in the retroperitoneum, between the abdominal aorta and inferior vena cava, on computed tomography. The patient underwent surgical excision of the tumor. Histological examination showed proliferating spindle cells in the clearly demarcated tumor; immunoreactivity for Kit and CD34 in tumor cells confirmed the diagnosis of GIST. The histological origin of GIST is suggested to be gastrointestinal pacemaker cells, because they share specific immunoreactivity for CD117/Kit, which is also relevant to pathogenesis of GIST. The present case was a rare primary GIST in the retroperitoneum with typical immunopathological features.