M cells are located in the follicle associated epithelium (FAE) of Peyer's patches (PPs) in the small intestine, where they mediate the uptake and transcytosis of luminal antigens to the underlying lymphoid tissue. Toll-like receptors (TLRs) have emerged as key mediators in the innate immune response by recognising pathogen associated molecular patterns (PAMPs) expressed by microorganisms. TLRs have previously been shown to be differentially expressed in the gastrointestinal tract. In this study PP were harvested from BALB/c mice. Ulex europaeus agglutinin 1 (UAE-1) positive M cells were isolated from FAE and the expression of TLR1-9 transcripts in M cells, FAE and villus epithelium (VE)was compared by quantitative real-time PCR. Transcripts for TLR1, TLR2 and TLR4 were found to be expressed at a high level in M cells in comparison to VE, with no transcripts being detected in the FAE. TLR3 and TLR6 were not found to be expressed in M cells or in the FAE. TLR5 and TLR7 were found to be expressed at a higher level in FAE compared to M cells. TLR9, which recognises unmethylated CpG DNA of bacteria and viruses and TLR8, which recognises ssRNA, were found to be preferentially expressed in M cells compared to FAE and VE. (C) 2009 Elsevier Ltd. All rights reserved.