The innate immune system is an ancient and diverse collection of defenses, including the recognition of pathogens through the use of germline-encoded pathogen receptors. The adaptive immune system, encompassing T and B cell responses, is a more recent development that utilizes somatically recombined antigen receptor genes to recognize virtually any antigen. The adaptive immune system has the advantage of flexibility and immunologic memory but it is completely dependent upon elements of the innate immune system for the initiation and direction of responses. Appropriate innate and acquired immune system interactions lead to highly efficient recognition and clearance of pathogens, but maladaptive interactions between these two systems can result in harmful immunologic responses including allergy, autoimmunity, and allograft rejection.