Mycophenolate mofetil (MMF) is a T-cell inhibitor frequently used in the treatment of acute allograft rejection. MMF may cause colitis that clinically and histologically resembles graft-versus-host disease (GVHD). The aim of this study was to evaluate a wide range of histologic features that may help differentiate MMF from GVHD-induced colitis and to validate significant features on a cohort of bone marrow transplant patients who were also taking MMF as part of their immunosuppressive regimen and developed a diarrheal illness due to colitis. Routinely processed colonic biopsies from 17 patients with MMF colitis and 40 patients with GVHD-induced colitis were evaluated for the overall grade of colitis (grades 1 to 4) and histologically for a wide range of inflammatory, epithelial, and architectural changes in a blinded manner. Statistically significant features were then tested in a cohort of 20 bone marrow transplant patients who also received MMF, and later developed a diarrheal illness. Both univariate and multivariate analyses (including receiver operating characteristic analysis) were performed. Morphologic features shown to be independently associated with MMF include the presence and quantity of lamina propria eosinophils and endocrine cell aggregates and the presence and quantity of apoptotic microabscesses, hypereosinophilic (degenerated) crypts, and crypt distortion. Eosinophils were present in all MMF patients, but apoptotic microabscesses were present in none and endocrine cell aggregates in only 1 case. When a grade-by-grade comparison was made between MMF and GVHD, grade 1 or 2 MMF also showed an increased prevalence rate and quantity of lamina propria neutrophils in comparison with grade 1 or 2 GVHD. By receiver operating characteristic analysis, a combination of lamina propria eosinophils >15 per 10 HPF, combined with a lack of endocrine cell aggregates and apoptotic microabscesses, revealed sensitivity, specificity, and positive and negative predictive values of 76%, 93%, 81%, and 90%, respectively, for identification of MMF colitis. On the basis of these data, we conclude that a variety of histologic features, in particular, eosinophils >15 per 10 HPF, lack of endocrine cell aggregates in the lamina propria, and lack of apoptotic microabscesses, can be used by pathologists to help separate MMF from GVHD-induced colitis in routine clinical practice.