Jejunal development occurs in a spatio-temporal pattern and is characterized by morphological and functional changes. To investigate jejunal development at the transcriptomic level, we performed microarray studies in 1-21-day-old chickens. Nine gene clusters were identified, each with a specific gene expression pattern. Subsequently, groups of genes with similar functions could be identified. Genes involved in morphological and functional development were highly expressed immediately after hatch with declining expression patterns afterwards. Immunological development can be roughly divided based on expression patterns into three processes over time; first innate response and immigration of immune cells, secondly differentiation and specialization, and thirdly maturation and immune regulation. We conclude that specific gene expression patterns coincide with the immunological, morphological, and functional development as measured by other methods. Our data show that transcriptomic approaches provide more detailed information on the biological processes underlying jejunal development.