A comprehensive understanding of the immune response is required to expand the range of vaccines available, as well as increase their efficacy and reduce side effects. Recent immunological breakthroughs in the understanding of the innate immune system and its role in shaping the immune response has lead to great interest in vaccines that selectively target innate immune pathways. Several well defined innate stimulators, such as TLR agonists, are now being developed to serve as adjuvants in the hopes of developing vaccines that induce safe, effective and sustained immune responses. Using a unique in vivo model of ovine pseudoafferent lymphatic cannulation, we investigated the innate response in afferent lymph following vaccination with Poly I:C and CpG. We have shown that cellular migration patterns differ between adjuvants, with Poly I:C inducing a greater neutrophil response when compared to CpG. In addition, CpG was shown to both increase the expression of MHC class II on antigen positive monocytes and induce greater antigen uptake by dendritic cells after vaccination. Further research with this cannulation model provides a unique opportunity to investigate the in vivo mechanisms underlying the action of adjuvants and contribute to the understanding of the complex immune response generated after vaccination.