Innate immune system could recognize the pathogen-associated molecular patterns by pattern-recognition receptors like Toll-like receptor (TLR) and nucleotide-binding oligomerisation domain (NOD) protein. Information regarding the structure and signalling pathways of TLRs and NODs could provide opportunities for new therapeutic approaches to modulate the innate immunity. Therapeutic targeting could be done by prevention of ligand binding to leucine-rich repeats domains of receptors, blocking the interactions between receptors (like Toll/interleukin-1 receptor domains of TLRs) and adaptors in signalling pathways, blocking the enzymes in signalling pathways, and immunostimulation with vaccine adjuvants. These therapeutic approaches could be useful in the treatment of different human diseases like immunological disorders, infections, and cancers. Further research on these receptors and their signalling pathways could help scientists to identify new candidates for therapeutic targeting.