Successful transplantation requires the establishment of an ongoing state in which there is simultaneous inhibition of the undesired T cell-dependent rejection response and yet retention of the ability to develop effective cell-mediated primary and memory responses to pathogens. The complexity of attaining such a precarious state is underscored by the growing body of evidence that alloreactivity can be profoundly influenced by infections that occur before, concurrent with, or subsequent to an organ transplant. In this review, we explore the growing list of mechanisms that have been identified by which pathogen-host interactions might influence rejection, including the degeneracy of TCR recognition leading to cross-reactive immune responses, the effects of pathogens on innate immune mechanisms, and the potential impact of virally induced lymphopenia.