Interaction of TLR9 with ligands activates NF-κB， leading to proinflammatory cytokine production. Excessive TLR activation is a pathogenic factor for inflammatory diseases. This study has examined cell-permeating decoy peptides (CPDPs) derived from the TLR9 Toll/IL-1R resistance (TIR) domain. CPDP 9R34， which included AB loop， β-strand B， and N-terminal BB loop residues， inhibited TLR9 signaling most potently. CPDPs derived from α-helices C， D， and E (i.e.， 9R6， 9R9， and 9R11) also inhibited TLR9-induced cytokines but were less potent than 9R34. 9R34 did not inhibit TLR2/1， TLR4， or TLR7 signaling. The N-terminal deletion modification of 9R34， 9R34-ΔN， inhibited TLR9 as potently as the full length 9R34. Binding of 9R34-ΔN to TIR domains was studied using cell-based Förster resonance energy transfer/fluorescence lifetime imaging approach. Cy3-labeled 9R34-ΔN dose-dependently decreased fluorescence lifetime of TLR9 TIR-Cerulean (Cer) fusion protein. Cy3-9R34-ΔN also bound TIRAP TIR， albeit with a lesser affinity， but not MyD88 TIR， whereas CPDP from the opposite TIR surface， 9R11， bound both adapters and TLR9. i.p. administration of 9R34-ΔN suppressed oligonucleotide-induced systemic cytokines and lethality in mice. This study identifies a potent， TLR9-specific CPDP that targets both receptor dimerization and adapter recruitment. Location of TIR segments that represent inhibitory CPDPs suggests that TIR domains of TLRs and TLR adapters interact through structurally homologous surfaces within primary receptor complex， leading to formation of a double-stranded， filamentous structure. In the presence of TIRAP and MyD88， primary complex can elongate bidirectionally， from two opposite ends， whereas in TIRAP-deficient cells， elongation is unidirectional， only through the αE side.