Patients who have undergone bone marrow transplantation (BMT) remain immunodeficient for months to years posttransplantation. To evaluate the basic molecular events underlying reconstitution of the humoral immune response, we have performed a detailed nucleotide sequence analysis of VH6 containing rearrangements in circulating B cells from two BM donor/recipient pairs. Our results show that the third complementarity determining region (CDR3) diversity is much lower early after transplantation, compared with that of the donors, and that the clonal variability remains low for 3 months. Repertoire diversification follows an oligoclonal pattern where B lymphopoiesis appears to occur in waves up to 6 months posttransplantation. The repertoire among donated marrow cells is not reflected in peripheral blood lymphocytes from the transplanted patients. There is differential D gene utilization among both donor and patient samples, whereas JH gene usage is biased toward JH4, 5, and 6. One month after transplantation the vast majority of the sequenced clones are functional and contain a high frequency of replacement mutations in the CDRs of the VH6 gene. We conclude that Ig gene expression is very restricted early after BMT and that development of the B-cell repertoire appears to follow a wavelike pattern.