Clostridium difficile infection is the leading cause of hospital acquired antibiotic-associated diarrhea in the US (Bartlett, 2006). The increased prevalence of circulating C.difficile strains poses a significant health threat to US health care facilities. Strains expressing the toxin C. difficile Transferase (CDT), in addition to Toxins A and B (TcdA and TcdB), are more virulent and associated with higher mortality rates (Bacci et al., 2011). We have recently identified a protective role for eosinophils against C.difficile pathogenesis (Buonomo et al., 2016). We have also defined CDT’s ability to increase host inflammation and suppress protective eosinophils through a TLR2 dependent mechanism (Cowardin et al., 2016). How CDT promotes virulence and eosinophil suppression via TLR2 is still under investigation. We employed a genome-wide microarray approach to reveal divergent transcriptional profiles between protected (TLR2-/-) and unprotected (WT) mice infected with either CDT expressing or CDT mutant strains of C. difficile. This work revealed novel host mediated TLR2-dependent inflammatory pathways to CDT. We provide an unbiased framework for understanding the host immune response to the binary toxin CDT produced by C. difficile and how TLR2 signaling enhances virulence.