Antithymocyte globulin Fresenius (ATG-F) is used before hematopoietic stem cell transplantation to prevent graft rejection and graft-versus-host disease in patients with HLA-matched unrelated donors or mismatched volunteers. However, little is known about the effect of ATG-F on the reconstitution of B-cell subsets. Sixty-seven patients were longitudinally studied at day 15, day 30, and then monthly after hematopoietic stem cell transplantation. Conditioning regimes included ATG-F, which was infused at days 3, 2 and 1 at a dosage of 10 mg/kg/d. Twenty-seven patients received conditioning regimes without ATG. ATG-treated patients showed a significant delay of CD19+ B cells in the early recovery period. The absolute numbers of circulating CD19+ B cells were significantly lower (P < 0.05) up to 5 months post-transplantation compared to non-ATG patients. The recovery of the memory compartment was delayed in both groups and did not reach normal values 1-year post-transplantation. ATG-treated patient showed significantly lower absolute numbers of circulating CD27+ memory B cells in the first-month after transplantation compared to non-ATG patients. In conclusion, treatment with ATG in the conditioning regime of patients undergoing allogeneic hematopoietic stem cell transplantation leads to a significant delay of CD19+ B cells. Thus, ATG seems also to negatively influence B-cell immune reconstitution.