Recurrence of Burkitt's lymphoma (BL)/acute lymphoblastic leukemia (ALL)-L3 after a long-term remission is very rare. We herein report on a case of BL/ALL-L3 indicating solitary recurrence in the tonsil after a 3-year remission. A 50-year-old man was diagnosed as having Burkitt's type ALL-L3 with involvement of the stomach and abdominal lymph nodes. He was treated with intensive chemotherapy consisting of methotrexate and cyclophosphamide (ALL-BFM86 protocol), and a complete remission was achieved. After sustaining the remission for three years, a swelling of the right tonsil was observed, which was histologically diagnosed as Burkitt's lymphoma. No other organ involvement, including the bone marrow, was observed. The pattern of c-myc rearrangement of the tonsil demonstrated by southern blotting was identical to that of the bone marrow at initial presentation and the recurrence of primary ALL-L3/BL was thus confirmed. The patient was then treated with the ALL-BFM86 protocol and subsequently underwent high-dose chemoradiotherapy with autologous peripheral blood stem cell transplantation (PBSCT). He has now been in complete remission for more than 2 years after his PBSCT.