While the Toll-like receptors (TLRs) are responsible for the recognition and response to pathogen ligands, increasing evidence suggests that the family of five cytosolic Toll/IL-1 receptor (TIR) adaptor proteins also play a crucial role in the specificity of the response. Genetic studies in mice, and increasingly in human polymorphic populations, have given us a greater understanding the role these adaptors play in orchestrating and coordinating the multifaceted immune response to multiple exogenous threats. Importantly, with growing evidence of the critical role TLRs play in responses to host danger signals and autoimmune disease, a more comprehensive understanding and appreciation of the role these adaptors play in disease progression may provide future targets for therapeutic intervention in human disease. Importantly, growing evidence supports the concept of pathway specific and inflammatory control by a better understanding of how these adaptors interact with other signalling mediators, where they localise within the cell and the inflammatory programs they initiate as a way of manipulating immune responses. This review deals with our current understanding of these TIR-containing adaptor proteins and how mutagenesis of specific residues and domains has increased our knowledge of their function in TLR immune responses.