Background: Antitumor necrosis alpha (TNFα) therapy is often used in the management of patients with inflammatory bowel disease (IBD) and may have effects on lymphoid tissue architecture and function. The goal of our study was to characterize the effects of TNFα inhibitors on mesenteric lymph node and mucosa-associated lymphoid tissue in patients with IBD. Methods: We examined lymphoid tissue morphology in IBD patients treated with TNFα inhibitors compared to untreated controls. Intestinal resections from 19 patients (10 anti-TNFα treated and 9 controls) were reviewed. Immunohistochemistry for CD21, CD20, and CD3 was performed on ileocecal valve lymphoid tissue and mesenteric lymph nodes from the resection specimens to assess follicular architecture. Results: Relative to control groups, TNFα-treated groups showed less preserved germinal center architecture, evidenced by lower overall semiquantitative scores for follicular architecture. Likewise, the percentage of secondary follicles to total follicles was decreased in patients treated with TNFα blockade. Conclusions: Our results suggest that TNFα inhibitors may play a role in disruption of lymphoid germinal center architecture in patients with IBD. Awareness of this disrupted lymphoid morphology when examining histologic sections from patients with IBD treated with TNFα inhibitors may prevent unnecessary studies to exclude a lymphoproliferative disorder.