Abstract Background Inducible nitric oxide synthase (iNOS) produces nitric oxide and modulates many biologic processes critical in the development of rejection; however, its role in chronic rejection (CR) in small-bowel transplantation (SBT) is largely unknown. Methods FK506 prevented acute rejection (AR); however, recipients eventually lost their bowel grafts to CR. Combined FK506 and rapamycin treatment prevented CR, thus leading to long-term graft survival. We investigated iNOS expression in our rat orthotopic SBT CR model. Results Histologically, mesentery vascular occlusion and fibrosis, which are hallmarks of CR, were apparent in bowel grafts in an FK506 single-treatment group. In contrast, patients with long-term surviving grafts receiving FK506 and rapamycin developed mild vascular occlusion and fibrosis. Unlike in AR, low iNOS expression, which is associated with decreased macrophage infiltration, was observed in CR grafts. However, iNOS expression and macrophage infiltration was higher in long-term–surviving grafts than CR grafts. Immunofluorescence staining revealed that the majority of macrophages expressed iNOS in long-term surviving grafts. Comments Sequential treatment combining FK506 and rapamycin prolonged survival of SBT animals with decreased vasculopathy and collagen deposition of the intestinal grafts. iNOS may play opposing roles in AR and CR in SBT.