Objective The purpose of this paper was to study the distribution frequency of immunoglobulin heavy chain gene(IgH) and T cell receptor (TCR)Vδ 2Dδ 3 gene rearrangement in children with acute lymphoblastic leukemia(ALL) in the first visit and the significance in early diagnosis of central nervous system leukemia(CNSL) and monitoring of MRD in CSF.Methods PCR and Nested-PCR techniques were employed to amplify IgH and TCR Vδ 2Dδ 3 fragments from blast cells in bone marrow and from CSF of patients with ALL.Results Twenty three of 32 patients had IgH gene rearrangement and/or TCR Vδ 2Dδ 3 gene rearrangement in bone marrow samples.Nine of 23 CSF samples from patients during remission induction had TCR Vδ 2Dδ 3 gene rearrangement and 4 samples had IgH gene rearrangement. Three of 37 CSF samples from patients in complete remission had IgH gene rearrangement and 7 samples had Vδ 2Dδ 3 gene rearrangement.Conclusions The positive rate of IgH gene rearrangement is 47% and that of Vδ 2Dδ 3 gene rearrangement is 38% in detected samples of bone marrow. Dynamic detection of IgH and Vδ 2Dδ 3 gene rearrangements in CSF of ALL patients by PCR techniques is an effective tool for early clinical diagnosis of CNSL and much more sensitive than CSF routine examination.It plays a guiding role in prevention and prognosis evaluation of CNSL.