Normal numbers of circulating B lymphocytes are reached during the first 6 months following allogeneic BMT, but humoral immunity remains poor. The molecular basis for this lack of function in the first appearing B lymphocytes has not been clarified. Accordingly, we have studied the reconstitution of the VH3 containing Ig repertoire in two CML patients transplanted with allogeneic BM and one healthy control. PBMCs were isolated at several time-points after BMT and mRNA was prepared. VH3 containing Ig rearrangements were amplified with RT-PCR and then cloned and analyzed with colony hybridization using complementary determining region 3 (CDR3)-specific oligonucleotide probes. Four weeks after BMT, two individual clones together represented 52% of the analyzed CDR3 regions. At 6, 8 and 12 weeks after BMT the corresponding probes hybridized with 2-6% of the colonies. A similar pattern was obtained for the other patient. In samples from the healthy control no clones were detected using CDR3-specific oligonucleotide probes from the control. We conclude that the VH3 containing Ig repertoire after BMT is oligoclonal and that specific rearrangements dominate at different time-points. This restriction of the B cell repertoire may contribute to the impaired humoral immunity observed in BMT recipients.