New therapeutic approaches for the treatment of B-cell chronic lymphocytic leukemia (B-CLL) can induce remarkable responses. Molecular remissions have been observed occasionally after high-dose chemotherapy. Thus, new improved techniques to monitor residual tumor cells on a molecular basis in CLL are warranted. For this purpose, a real-time quantitative allele-specific oligonucleotide polymerase chain reaction (ASO-PCR) for patients with B-CLL was designed. In the present study, the PCR assay was standardized with identical cycling parameters as well as primer, probe, and MgCl(2) concentration for each patient. Ten patients were monitored with DNA samples obtained at 52 time points (median: 5.2 per patient). The median follow-up per patient was 11.4 months. Nine of ten patients had PCR-detectable residual tumor cells in the peripheral blood after therapy. One patient became PCR negative with a combination of fludarabine and rituximab after the end of treatment. The MRD levels in patients with detectable disease ranged from 0.002% to 10.1% after therapy. We conclude that real-time quantitative ASO-PCR can be utilized for quantitative molecular monitoring of minimal residual disease (MRD) in B-CLL patients in complete remission (CR), that new effective treatment approaches such as combined chemo/immunotherapy can render CLL patients PCR negative, and that different MRD levels in PCR-positive patients were observed warranting further investigation into possible correlation with clinical outcome.