There is a constant interplay between the innate and adaptive immune systems, which leads to a protective immune response against pathogens and contributes effectively to self-non-self discrimination. Toll-like receptors (TLRs) are key components of the innate immune system, which activate multiple inflammatory pathways and coordinate systemic defense against pathogens. In addition to recognizing unique molecular patterns associated with different classes of pathogens, TLRs may also recognize a number of self proteins and endogenous nucleic acids. Data originating predominantly from animal models of autoimmune disease and circumstantial data from human patients suggest that inappropriate activation of TLR pathways by endogenous or exogenous ligands may lead to the initiation and/or perpetuation of autoimmune responses and tissue injury.