Imatinib has revolutionized the treatment and prognosis of patients with gastrointestinal stromal tumors (GIST). In contrast to liver and/or abdominal involvement, bone metastases are an uncommon event in GIST. We report here two patients with metastatic GIST who developed pelvic bone marrow focal lesions visible on MRI examinations, while Imatinib dramatically improved other tumor sites. A biopsy in one patient diagnosed bone marrow necrosis. The other patient had a favorable follow-up over several years, without bone metastases. Focal bone marrow abnormalities, detected on MRI examinations and mimicking bone metastases in patients who were otherwise responding, should be considered as probable bone marrow necrosis.