Ovine pulmonary adenocarcinoma (OPA) is a chronic respiratory disease of sheep caused by Jaagsiekte sheep retrovirus, with important economic and welfare implications worldwide. The virus infects respiratory epithelial cells and initiates oncogenesis and tumour growth. Due to the lack of detectable immunological response at any stage of disease no effective preclinical test or vaccine to control spread of disease is currently available. OPA is also considered to be a good animal model for human lung cancer. As in sheep, clinical presentation in humans does not appear until tumour growth is extensive by which time treatment is usually unsuccessful. This makes it difficult to study the early stages of disease, and detect potential markers for early diagnosis or therapeutic targets. Thus, the aim of the current study is to investigate the pathogenesis of the disease at the gene expression level. Whole transcriptome profiling was performed on lung samples derived from virus infected and uninfected specific pathogen free lambs, using RNAseq on the Illumina platform. Sequence reads were mapped to the currently available version of the sheep genome using TopHat and a gene-list of 1,127 differentially expressed genes was revealed between the two groups. Pathway and network analysis was followed using Ingenuity pathway analysis software and BioLayoutExpress3D, respectively. The top significant differentially expressed pathways of the upregulated transcripts were related to immune response to stimulus and wound healing, tumorigenesis, epithelial cell differentiation and tissue development. Several genes involved in these biological processes were confirmed with immunohistochemistry and RT-qPCR and have already been shown to play an important role in human lung cancer (CSF2, AGR2, CD163, LGM). Together, this analysis provides us with important information regarding the pathogenesis of OPA at a transcriptional level and reveals new insights into the use of sheep as an animal model for human lung adenocarcinoma.