Toll-like Receptors (TLRs) are key mediators of immune responses to infection. Upon microbial detection, these receptors activate inflammatory signal transduction pathways that involve IκB kinases, mitogen activated protein kinases, ubiquitin ligases and other adaptor proteins. Current models suggest these signaling proteins operate within functionally distinct multiprotein complexes, which are all activated by a receptor-proximal complex known as the myddosome. The mechanisms that connect the effector protein complexes in the TLR pathways are undefined. To define TLR pathway activities, we engineered macrophages to enable proteomic analysis of the endogenous myddosome constituent MyD88 and its interacting proteins. Proteomics demonstrated that myddosomes contain proteins that act at all stages and regulate all effector responses of the TLR signaling pathways.