Since the identification of Toll-like receptors, our knowledge about pattern-recognition receptors (PRRs) has increased rapidly. Classes of PRRs that have been recently discovered include RIG-I-like receptors, Nod-like receptors, and C-type lectin receptors. Recent studies have started to clarify the molecular basis of PRR-ligand interactions, yet the numbers of PRRs and their ligands continue to increase. New technologies have elucidated the network regulation of immune responses at the cellular and in vivo levels. We review the most recent discoveries about PRRs and their ligands, their roles in intracellular and in vivo regulation of immune responses, and the systems biology of innate immunity.