To detect and monitor tumor cells in the bone marrow (BM) or peripheral blood (PB) of patients with B cell lymphoma, we used the PCR-mediated RNase protection assay to identify the complementarity determining regions (CDR)-III gene rearrangement. This method required neither determination of nucleotide sequences nor construction of tumor-specific oligonucleotide probes or primers. The sensitivity of this assay using B cell lines as well as clinical samples revealed one tumor cell in a background of 10(4)-10(5) normal cells. Using this assay we examined 31 patients with B cell lymphoma in whom an IgH rearrangement of initial tumor tissues was confirmed by Southern blot analysis. Twenty of 31 (65%) patients were able to be analyzed using this assay. Tumor cells in the BM and PB evident on routine morphological examination or surface marker analysis were confirmed by this assay in all the evaluable samples. Moreover, we detected tumor cells in the BM or PB of five patients in whom no tumor cells were identified by conventional methods. The PCR-mediated RNase protection assay is useful to detect minimal residual disease (MRD) in B cell lymphoma because it is highly sensitive, rapid and simple.