Optimal gut function is of importance to the whole metabolism of a chicken and thus also central to efficient feed conversion and optimal meat and egg production. State-of-the-art Omics technologies are currently available to gain a deeper insight into animal physiology. This chapter summarizes the latest studies using different omics technologies (e.g. genomics, transcriptomics, proteomics, metabolomics) to identify the response of chicken intestinal cells to various effectors. First, the functions, physiology and microbiota of the gastrointestinal tract in chicken are discussed. Then follows a section on Omics technologies, how they can be used and what they can tell researchers. The authors then present a section on the application of omics to the study of the chicken intestine. The chapter concludes with a case study on the proteomic analysis of the mucosal layer of the chicken gut, and a look to future trends in research.