Peripheral administration of lipopolysaccharide (LPS) induces follicular atresia via toll-like receptor 4 (TLR4) signalling, resulting in primordial follicle destruction. Although the effects of LPS on sexually-mature animals are well known, the effects of LPS exposure during the early neonatal period, a time which corresponds to the establishment of primordial follicle reserve, have not been investigated. In the current study, in vivo effects of neonatal LPS exposure were examined on ovarian gene expression. Wistar rats were administered with 0.05mg/kg of LPS (Salmonella Enteritidis) or treated as saline-controls, on postnatal days 3 and 5 (Birth=day 1). On day 7 ovaries were collected for microarray analysis, which was confirmed via subsequent qRT-PCR. Western blotting and immunofluorescence were also performed on a selected number of proteins. Microarray analysis revealed a significant increase in the expression of 710 genes (≥ 2-fold change, p<.05). Altered genes were identified as components of several molecular networks involving the inflammatory response, immune signalling and reproductive development. Canonical pathway analysis identified a number of pathways involved in immune function, of which LPS-stimulated mitogen-activated protein kinase (MAPK) signalling pathway was chosen for further examination. The expression of TLR4 transcript, a major component of this pathway, was significantly upregulated in both microarray and qRT-PCR analyses (p<.05). TLR4 protein expression was also significantly increased in the ovaries of LPS-treated animals (p<.05). The data suggests that peripheral administration of LPS during the early neonatal period in rodents, results in the activation of ovarian TLR4 signalling. As the formation of primordial follicles is not established until PND 3 in our animal model, we propose that an immune challenge at this time point may directly intervene with the formation and establishment of the finite primordial follicle pool via activation of inflammatory pathways.