Background. The optimal biopsy site of bowel allografts for rejection surveillance remains controversial. We compared the results of jejunal (JBx) and ileal (IBx) biopsies after bowel transplantation in a porcine model. Methods. Eighteen Yorkshire-Landrace pigs served as donors. Eighteen recipient pigs underwent total enterectomy followed by orthotopic small bowel transplantation with or without the colon. A jejunostomy and a Bishop-Koop ileostomy were constructed for biopsies. Immunosuppression consisted of FK506 (target level 10-15 ng/ml by enzyme immunoparticle assay) and prednisone administered via the jejunostomy. Simultaneous JBx and IBx were performed twice weekly. Acute rejection was graded as mild, moderate, or severe based on previously published criteria. Results. Mean overall survival after the transplant was 17.4 days. A total of 162 specimens were collected and evaluated for rejection (JBx, 81; IBx, 81). Acute rejection was detected in 41 JBx cases (50.7%) and 40 IBx cases (49.4%). The presence or absence of rejection was concordant between JBx and IBx in 70 of 81 case pairs (86.4%). Of the 11 discordant case pairs, 6 were JBx positive/IBx negative, whereas 5 were JBx negative/IBx positive. A total of 35 case pairs were synchronously positive, 24 (68.8%) of which demonstrated the same degree of rejection. Conclusions. The correlation between JBx and IBx of bowel allografts in diagnosing the presence of acute rejection is quite good. However, performing IBx alone would have missed about 7.5% of the rejection episodes. Because the early treatment of rejection in bowel transplantation is of paramount importance, in selected cases, biopsies from both the ileum and jejunum should be considered if technically feasible.