Background: Costimulatory blockade plus donor-specific transfusion (DST) induces long-term graft acceptance, however the mechanism by which this tolerance occurs remains incompletely defined. The lymph node (LN) contains a basic scaffolding structure comprised of collagens, laminins and stromal fibers such as ER-TR7. These fibers form a protein meshwork foundation for cell interactions and bind chemokines that guide cells to specific, instructive microdomains. This study tested the hypothesis that tolerance induction or immunization involves modification of lymph node structure and chemokine expression, which affect the localization of graft reactive T cells. Methods: Tolerance was induced by treating C57BL/6 mice with BALB/c DST + anti-CD40L mAb, while immunity was induced by treating mice with DST only. Mice were euthanized 12 hours to 7 days post-treatment and LNs were studied by quantitative immunohistochemistry or quantitative RT-PCR to define the amount and location of the structural elements collagen III, ER-TR7, desmin, laminin, the chemokines CCL19 and CCL21 and localization of graft reactive cells. Results: LN in tolerant and immune mice displayed distinct structural modifications and chemokine expression. In the LN of tolerant mice, ER-TR7 increased and peaked at day 5 post-tolerance induction while, it remained close to levels observed in naive LNs following immunization. Following tolerance induction or immunization, an increase in laminin, desmin and collagen III occurred. With respect to chemokines, CCL19 presence increased gradually after day 3 in tolerant mice. In contrast, CCL19 presence peaked at day 3 in immune mice. Interestingly, CCL21 presence decreased following both tolerance induction and immunization. At 12 hours post treatment, LN follicular reticular cells (FRCs) from tolerant LNs seemed to express higher amounts of CCL21 as compared to immune FRCs that expressed CCL19. Graft reactive cells accumulated gradually in LN cortical ridge and T cell areas for tolerant LNs as compared to immune LNs. Conclusion: Tolerance induction results in structural changes within the LN. ER-TR7 and laminin are essential LN structural stromal fibers, and CCL19 is important for T cell and dendritic cell LN chemoattraction. These results suggest that tolerance induction leads to changes in both LN structure and function. These changes can subsequently affect T cell migration, homing and differentiation in the LN. Hence, this remodeling choreographs the encounters and interactions between antigen reactive cells and their cognate antigen resulting in tolerance as opposed to immunity. These findings suggest that the LN is a malleable structure, and changes in both physical structure and chemokine expression affect LN function.