Toll-like receptors (TLRs) are a subgroup of pattern recognition receptors (PRRs), which recognize molecular patterns expressed by different microorganisms. Although much is known about how TLRs function, substantial gaps in our knowledge still prevent the definition of a complete picture of TLR signaling. However, several recent studies describe additional layers of complexity for the regulation of TLR signaling, including (1) the structural biology of TLR ligand recognition, (2) the cell biology of TLR adaptor recruitment, (3) the interplay between post-translational modifications of signaling proteins, and (4) the newly described, autonomous role of the TLR4 coreceptor CD14. In this review, the authors update our current knowledge on the structural biology and ligand recognition strategies of TLRs.