The aim of this study was to use clonal gene rearrangements assays to discriminate between oligo-clonal or polyclonal reactive processes in cases that presented difficulty in diagnosis of B or T-acute lymphoblastic leukemia (ALL) due to abnormal phenotypes detected by flow-cytometry. Monoclonal B /T cells were detected by rearrangements of immunoglobulin (Ig) and T-cell receptors (TCR) in 10 patients. After DNA extraction from peripheral blood, multiplex PCR was used to amplify the Ig/TCR gene rearrangements followed by capillary electrophoresis, according to BIOMED 2 conditions. The evaluation of the results was carried out in the clinical and interdisciplinary (histomorphological, molecular and flow-cytometric) context. The presence of clonal rearrangements may indicate the existence of two neoplastic processes or a single clone with two gene rearrangements � one productive and one non-productive on the two alleles, considering the use of genomic DNA. By fragment analysis we identified B/T cells gene recombinations using multiplex PCR with primer sets that target each type of gene family. Using these molecular markers we can discriminate between monoclonal/polyclonal cells and follow a clonal marker throughout the disease evolution.