Polymerase chain reaction (PCR) techniques utilizing clonospecific T cell receptor (TCR) gamma or delta junctional regions constitute broadly applicable strategies to study the clinical relevance of minimal residual disease (MRD) in acute lymphoblastic leukemia (ALL) patients. For the majority of cases current PCR protocols allow the reliable detection of one neoplastic cell among 10(4) to 10(6) normal counterparts. Occasionally, however, PCR analysis fails to reach this level of sensitivity. Here we demonstrate by means of three representative ALL cases how modifications of PCR protocols can overcome some of the limitations. Thus usage of biotinylated PCR products of TCR delta junctional regions and their direct application as templates for the generation of clonospecific probes allows the introduction of a selection step and results in a significant reduction of unspecific background signals. According to our experience as well as data from other laboratories we also recommend the usage of synthetic oligonucleotides representing TCR gamma junctions as clone-specific primers for a consecutive round of amplification rather than as clonospecific probes. Both modifications improve and facilitate the detection of MRD in leukemias characterized by TCR gamma and TCR delta recombinations.