OBJECTIVE: Exploring the detection of minimal residual malignant cells in bone marrow from children with hematological malignancies to predict the prognosis. METHODS: Seventy-five patients with acute lymphoblastic leukemia (ALL), stage IV non-Hodgkin's lymphoma or stage IV neuroblastoma were studied. Complete remission was maintained for over 3 months before the detection. Minimal residual disease was detected by polymerase chain reaction (PCR) for IgH and TcRgamma rearrangements in lymphoid tumors by reverse transcriptase-polymerase chain reaction (RT-PCR) for neuroblastoma patients. RESULTS: Thirty five patients were positive for minimal residual disease, and 21 of them (60%) relapsed 3 - 40 months later, while only 7 (17%) negative patients relapsed (chi(2) = 12.59, P < 0.01). CONCLUSION: Minimal residual disease detection in bone marrow by PCR might predict prognosis in some childhood hematological malignancies.