Multiple myeloma is characterized by malignant plasma cell-infiltration of bone marrow. Treatment with high-dose therapy results in a high rate of clinical remissions, but almost all patients ultimately relapse. Clinical staging and detection of relapse are limited in sensitivity. Therefore, we established molecular methods based on the highly clone-specific CDR regions of the immunoglobulin VH locus for sensitive and specific detection of residual myeloma cells after bone marrow transplantation. VDJ rearrangements were identified using a set of VH primers and a JH primer. Clone-specific rearrangements were detected by comparison with germ-line sequences. With the nested PCR approach, first-round amplification with the consensus primers was done followed by second amplification with myeloma-specific primers. The real-time quantitative PCR was performed using a myeloma-specific forward primer in combination with a JH consensus TaqMan probe and reverse primer. Sensitivity was tested using dilutions of myeloma cell lines into mononuclear cells. Nested PCR had a sensitivity of 10(-6) and TaqMan PCR of 10(-4) to 10(-5). Specificity was determined by testing different cell lines and patients' probes. These results were confirmed by follow up of 2 patients after allogeneic transplantation with dose-reduced conditioning. Molecular methods are very sensitive and specific tools for follow up of myeloma patients after allogeneic transplantation. By using the quantitative approach, it is possible to see kinetics of bone marrow tumor load, which can be used to guide therapeutic decisions like donor leukocyte infusions (DLI).