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Surgical treatments including radical resection and local excision remain the main treatment for primary rectal gastrointestinal stromal tumors (GISTs). However, since patients with high-grade rectal GISTs have a higher risk of tumor recurrence and a shorter life expectancy, neoadjuvant treatment is necessary. In this case report, the efficacy of imatinib mesylate (IM) as a neoadjuvant therapy was assessed in an old man with malignant rectal GIST. The patient received IM preoperative treatment for a short period of one and a half months; at the end of the IM treatment, computed tomography scanning showed a markedly reduced tumor size and cystic changes of the tissue. At that time, a function sphincter-sparing surgery was performed. The histological examination of the resected specimen detected no tumor cells, but residual blood vessels and scattered inflammatory lymphocytes. After surgery, the patient has been followed up without additional IM treatment and remained disease-free for 57 mo. This case indicates that IM neoadjuvant therapy can dramatically improve the prognosis of rectal malignant GIST.