Although the prognosis of clear cell sarcoma of the kidney (CCSK) has improved, when metastases occur the probability of cure is very low. We have treated two pediatric patients with relapsed CCSK, one with multiple bone metastases and another with brain metastases. After one or two courses of re-induction chemotherapy and radiation therapy to the sites of metastasis, they received double high-dose chemotherapy with autologous bone marrow rescue. Conditioning regimens were ifosphamide plus melphalan for the first autograft and busulfan plus thiotepa for the second. Hematological recovery was prompt, and no severe complications were observed. They are doing well without evidence of recurrence at 19 and 49 months after the second autograft, respectively.