Alemtuzumab, a humanized CD52 monoclonal antibody (mAb), has been used for immune induction in clinical small bowel transplantation (SBT). However, the local impact of CD52 mAb on the transplanted intestine is not known. In this study, we investigated the effects of CD52 mAb on the intestinal intraepithelial lymphocytes (iIELs) in grafts using a murine orthotopic SBT model. The antimouse CD52 mAb was used as a surrogate antibody. Graft rejection was assessed by histopathologic analysis, iIELs were isolated for flow cytometric analysis, the mucosal keratinocyte growth factor (KGF) expression was evaluated by real-time polymerase chain reaction, and epithelial cell (EC) proliferation (percent bromodeoxyuridine incorporation) was measured by immunohistochemistry. No mice showed evidence of rejection. Seven days after SBT, when the CD52 mAb was used, the numbers of iIELs and both T-cell receptor (TCR) γδ+ and TCRαβ+ subpopulations were decreased, and the number of TCRγδ+ iIELs of donor origin was prominently reduced in the allografts. Furthermore, TCRγδ+ iIEL–derived KGF messenger RNA expression and EC proliferation decreased significantly after CD52 mAb application. These data demonstrate that the antimouse CD52 mAb could deplete iIELs in the transplanted intestine, especially the TCRγδ+ subset of donor origin. The reduction of TCRγδ+ iIELs accompanied the decrease in mucosal KGF expression and EC proliferation, which may slow down the epithelial turnover and retard the repair of the damaged epithelium.