The innate immune system is an ancient, conserved pathogen response system that lays the foundation for self/non-self discrimination. The cells of the innate immune system are responsible for recognizing the highly conserved molecular motifs of microbial pathogens and represent the first line of immunological defense as well as contributing to the activation of the adaptive immune response. Toll-like receptors are a family of 13 germline-encoded receptors on antigen presenting cells, T cells and various non-lymphoid tissues that are critically important for innate immune function and inflammatory responses. Furthermore, numerous clinical and experimental animal studies have demonstrated the importance of Toll-like receptors as well as members of their signaling pathways in the setting of organ transplantation, where endogenous ligands may play a significant role. Toll-like receptor signaling has the capacity to inhibit transplantation tolerance. A complete understanding of the relationship between Toll-like receptor signaling and transplantation tolerance is essential to modifying, reducing or abrogating immune suppression as well as improving patient outcomes.