Footrot is characterised by interdigital dermatitis (ID) and by the separation of the skin and hoof horn, called under-running lesions (footrot). This disease is of greatest welfare and economic concern for veterinarians and sheep farmers worldwide1. Dichelobacter nodosus is the causative agent of footrot2, but its role in ID is not fully understood. The severity of footrot is thought to be exacerbated by the intense inflammatory response; however, there is little information regarding the immune responses to footrot. In this context, the hypothesis of this study is that the pathology of footrot is a host-mediated over-expression of local immune responses in the skin leading to severe inflammation in the foot that can progress to hoof horn separation from underlying tissues. The aim of this study is to investigate the relation between D. nodosus and eubacteria load and host mRNA expression of immune molecules in healthy, ID and footrot samples. Here we present results on eubacterial and D. nodosus colonization in relation to disease state and foot conformation. Sheep feet were scored for conformation, ID and footrot lesions (post slaughter). Biopsy samples (n=198) were collected from the skin-hoof interface and quantitative PCR (qPCR) was used to quantify eubacteria and D. nodosus. All biopsy samples showed similar levels of bacterial colonization. The highest prevalence and load of D. nodosus were on feet with moderate to severe ID, highlighting that D. nodosus load might have a role in the early stage of the disease (ID), contributing to the progression to footrot. D. nodosus load increased from healthy to ID scores, but not in footrot scores, confirming that the D. nodosus load is not related to the presence and severity of under-running lesions. The association between the bacteria load and immune molecule expression (RNASeq) will generate more detailed information of the disease process.