Salmonella typhimurium is a gram-negative enteric pathogen that invades the mucosal epithelium and is associated with diarrheal illness in humans. Flagellin, from S. typhimurium and other gram-negative bacteria, has been shown to be the predominant pro-inflammatory mediator through activation of the basolateral Toll-like receptor 5 (TLR5). Recent evidence has shown that prior exposure can render immune cells tolerant to subsequent challenges by TLR ligands. Accordingly, we examined whether prior exposure to purified flagellin would render human intestinal epithelial cells insensitive to future contact. We found that flagellin-induced tolerance is common to polarized epithelial cells, prevents further activation of pro-inflammatory signaling cascades by both purified flagellin and Salmonella bacteria, but does not affect TNF stimulation of the same pathways. Flagellin tolerance is a rapid process that does not require protein synthesis, and occurs within 1 to 2 hours of flagellin exposure. Prolonged flagellin exposure blocks activation of NFB, MAPK and PI3K signaling pathways, and results in the internalization of a fraction of the basolateral TLR5 without affecting the polarity or total expression of TLR5. After removal of flagellin cells require more than 24 hours to fully recover their ability to mount a normal proinflammatory response. We have found that activation of PI3K and Akt by flagellin has a small damping effect in the early stages of flagellin signaling, but is not responsible for tolerance. Our study indicates that inhibition of TLR5-associated IRAK-4 activity occurs during the development of flagellin tolerance and is likely the cause of tolerance.