Recent advances in the use of high throughput deep sequencing of RNA (RNAseq) have revolutionized the study of gene expression and have allowed unprecedented examination of the whole transcriptome of bacterial pathogens. While this technology has allowed rapid advancement of the molecular pathogenesis of disease in the model bacterial species such as E. coli and Salmonella, there remains minimal published data on the transciptome of the zoonotic pathogen Campylobacter jejuni, particularly in regard to exposure to the host environment. With the recent emergence of the highly virulent C. jejuni sheep abortion clone IA 3902 as the dominant cause for sheep abortion in the United States and increasingly frequent isolate from human outbreaks of foodbourne gastroenteritis, further understanding of the molecular mechanisms that allow for disease and persistence within the animal host of this particular strain is especially important. By utilizing a novel in vivo host model, we thus exposed C. jejuni IA 3902 to the bile-rich ovine gallbladder for up to 24 hours and were able to collect high quality total RNA following exposure. High throughput deep sequencing of strand specific rRNA-depleted total RNA was then performed on the Illumina Hi-Seq platform to characterize the transcriptome of IA 3902 and Rockhopper was used to analyze differences in gene expression. Our results indicated a large number of protein coding genes differentially expressed in the in vivo gallbladder environment along with differential expression of several previously identified small non-coding RNAs. This research provides valuable insights into the mechanisms that may be utilized by C. jejuni to induce disease and develop a carrier state within the inhospitable host gallbladder environment.