Foreign nucleic acids, the essential signature molecules of invading pathogens that act as danger signals for host cells, are detected by endosomal nucleic acid-sensing toll-like receptors (TLRs) 3, 7, 8, 9, and 13. These TLRs have evolved to recognize 'non-self' nucleic acids within endosomal compartments and rapidly initiate innate immune responses to ensure host protection through induction of type I interferons, inflammatory cytokines, chemokines, and co-stimulatory molecules and maturation of immune cells. In this review, we highlight our understanding of the recognition of pathogen-associated nucleic acids and activation of corresponding signaling pathways through endosomal nucleic acid-sensing TLRs 3, 7, 8, 9, and 13 for an enormous diversity of pathogens, with particular emphasis on their compartmentalization, intracellular trafficking, proteolytic cleavage, autophagy, and regulatory programs.