Several genes linked to immune function are differentially expressed in reproductive tissues and immune cells in models of greater and lesser fertility. As a model of poor fertility, we studied peripubertal animals, where embryo loss is approximately twice that observed in adult animals. A significant proportion of this loss occurs very early in pregnancy, by day 4, therefore, we focused on the isthmus of the oviduct, comparing gene expression in peripubertal animals to adult animals. Potential differential expression for proteins involved in steroid hormone signalling, growth factors and proteins important for immune function were observed. Several genes, including growth factors and receptors as well as interleukins and their receptors, were correlated to concentrations of progesterone and oestradiol. To better understand the potential importance of the immune system during very early pregnancy, and how the local immune system may change in response to an embryo, we examined how the local and peripheral immune system differed between non-pregnant and pregnant ewes. Principal component analysis revealed separation of function of local and peripheral lymph nodes, providing evidence of specialisation of function of the immune system around the reproductive tissues to facilitate establishment of pregnancy. Analysis revealed an effect of pregnancy on gene expression in both lymph nodes and reproductive tissue. Analysis of gene categories revealed that expression of genes of the T cell receptor pathway in reproductive tract tissues was associated with pregnancy status. Thus, differential gene expression observed between pregnant and non-pregnant animals is consistent with specialisation of immune function of the reproductive tract to facilitate establishment of pregnancy. The importance of the T-cells for early pregnancy was highlighted through pathway analysis.