The minimal residual disease (MRD) detection by the polymerase chain reaction (PCR) in children with acute lymphoblastic leukemia has been pointed to be an adverse prognostic factor. Detection methods based on this technique using clone-specific primers are cumbersome and time consuming. The detection of monoclonal gene rearrangements of gamma T-cell receptors (TCRgamma) is a simpler although less sensitive method. In the present study, we analyzed the presence of MRD during four different phases of treatment (week 4; 3-6, 12-24 months, and end of treatment) in 34 Brazilian children with lymphoid leukemia by three detection methods based on the PCR technique: (1) using consensus primers for the detection of a clonal population for TCRgamma; (2) clone-specific primers for the junctional region of TCRgamma; and (3) a semi-nested reaction with an initial cycle with consensus primers followed by a second cycle with clone-specific primers. MRD presence was associated with a shorter event-free survival and was the major independent prognostic factor in most of the phases analyzed. The use of consensus primers for the detection of TCRgamma clonality, although less sensitive, proved to be a simpler, faster and less costly method whose positivity was associated with more than 90% relapse rates during all phases analyzed.