The first part of my project involved the cloning, sequencing and analysis of genes for the ten sheep TLRs, adapter molecules and C-type lectins; this facilitated the development of quantitative, real-time RT-PCR assays for the accurate measurement of gene transcripts. Initial experiments used these assays to quantify innate receptor transcript levels in a range of tissues from clinically healthy adult sheep; in the distinct peripheral blood lymphocyte populations and the two afferent lymph dendritic cells subsets. The spleen, lung and lymph nodes express all TLRs; the kidney expresses high levels of TLR1, 2, 3, 4, 5, 6, but very low levels of TLR8, 9 and 10. The skin expresses low levels of TLR5, 6, 9 and 10 mRNA. CD172a+ DC express TLR3, 4 and 9 while CD172a- DC are Dectin-2 negative, TLR3+/-. To explore PRR expression in foetal immune system, second trimester foetal skin and spleens were collected for PRR mRNA expression determination. Foetal spleens have comparable levels of PRRs except for CD14. Significant differences were observed with TLR1, 4, 5, CD14, CARD15 and Dectin-1 between foetal and adult skin tissues. These baseline data allow deviations from normal to be identified in diseased states, Johne’s disease (JD) is a chronic disease of ruminants caused by Mycobacterium avium paratuberculosis (Map) and has three clinical forms – asymptomatic, paucibacillary or multibacillary associated with different types of immune response possibly influenced by the particular innate receptors. Consequently the differential pattern of PRR expression in the three forms of JD might be crucial to the pathogenesis of Map. Results from the present study show the importance of the following PRRs in ovine Johne’s disease discrimination; TLR2, CD14, TLR8, CARD15(NOD2), dectin-1 and dectin-2. These findings provide an insight into one facet of Map innate immune recognition and help to elucidate new target genes for possible mutation analyses and disease genotyping.