Previous work form our group has shown that innate immune cells perceive cigarette smoke as an inflammatory and xenobiotic stimulus, which alters the immune response to invading pathogens. It is unclear as to the specific cellular and molecular mechanisms driving cigarette smoke-induced inflammation, but we have demonstrated that this response is, in part, driven by Toll-Like Receptor (TLR) 2 in innate immune cells in vitro and in mice in vivo . Methodology/Principle findings: To address the impact TLR2/6, has on cigarette smoke-induced gene induction, HEK293 cells were permanently transfected with TLR2/6 or Null vector, and were stimulated with 10% cigarette smoke extract (CSE) for 8 h. Total RNA was extracted and the transcriptome analysed using Illumina Bead Chip arrays. In HEK293 Null cells, CSE induced 33 genes and down-regulated 41. In HEK293 TLR2/6 cells, CSE induced 23 genes and down-regulated 44. Further analysis revealed that 42 genes were regulated in a TLR2/6-dependent manner. Comparison of these genes with those induced by smoke in human primary monocytes revealed that 5 were mutually regulated. The major pathways affected were those associated with anti-oxidant pathways, tumorgenesis and cell survival. Conclusions: Our data suggest that the innate immune receptor TLR2/6 has a critical role for the expression of a particular cassette of genes induced by cigarette smoke. Pathway analysis indicates these are related to functions in both cell survival and tumorgenesis. Future validation of the relative importance of these pathways using more complex models is required a may lead to improved understanding of the pathology of cigarette smoke-induced diseases such as COPD, cardiovascular disease and cancer.