A certain quantity of residual leukemic cells at several time points during chemotherapy of childhood acute lymphoblastic leukemia (ALL) was proved to predict outcome. Future childhood ALL treatment will take minimal residual disease (MRD) into consideration for stratification aiming at an individualization of chemotherapeutic regimens. Recently, the first quantitative real-time PCR assay for MRD detection was described using T cell receptor and immunoglobulin gene rearrangements as clonal markers. Quantitative real-time PCR was performed with TaqMan technology. Here, we present for the first time the potential of LightCycler real-time PCR technology to quantify MRD. We compare and assess different approaches for real-time PCR quantification of leukemic cells, based either on clone-specific primers and general fluorescence detection with SYBR Green, TaqMan probe or hybridization probes, or based on general PCR amplification and clone-specific detection with hybridization probes. MRD quantification with LightCycler real-time PCR technology is a sensitive, specific and incomparably rapid method that needs no post-PCR handling, hence eliminating contamination risk and saving time. Working towards the establishment of MRD quantification in routine diagnostics and towards treatment strategies based on these results, LightCycler quantitative PCR seems to be a promising new technique that makes results immediately available for treatment decisions.