OBJECTIVE Rejection results in destruction of the intestinal mucosa. This is the major cause of morbidity and morbility in human allografts. The aim of this study was to investigate histomorphometric changes in both the graft and recipient intestinal mucosa after experimental orthotopic small bowel transplantation. METHODS Using the pig model, 21 large-white pigs underwent: laparotomy (n = 7) (control group); orthotopic small bowel transplantation without immunosuppression (n = 7); and orthotopic small bowel transplantation with cyclosporine A (n = 7). RESULTS 1) Significant reduction of total mucosal thickness (villi plus crypt) (p < 0.05) in both the graft and recipient mucosa; 2) Attenuation of this effect by administration of cyclosporine A, which reduced the loss of mucosal thickness mainly at the expense of crypt hipertrophy. CONCLUSIONS These findings suggest that villi and crypt length measurements may be a reliable method for monitoring rejection after small bowel transplantation.