A more in-depth exploration of gut functional aspects may be interesting in order to provide hints for action (e.g. dietary strategies) to favor gut balance maintenance (Sinha et al., 2017), given the important role of the intestine in development of possible metabolic diseases. A careful survey on the differential gene expression may help to scouting new interesting functions and identify potential markers for testing various experimental factors. The transcriptomes of the jejunum and cecum mucosae of 19 broiler chickens were compared. At slaughter age (day 42), on 38 birds, selected with a homogeneous body weight, jejunum and cecum mucosae were collected by gently scraping after tissues rinsing in PSB to remove residues of digesta, and immediately frozen in liquid nitrogen and then stored at -80°C. From both tissues, total RNA was extracted using GeneJET RNA Purification Kit (Thermo Scientific) Overall design: The analysis of whole mRNA transcript expression was done by Affymetrix© GeneChip Chicken 1.0 ST Array and hybridized arrays were scanned on Affimetrix© GeneChip Scanner 3000 7G System (Affymetrix, Santa Clara, California, USA). Data analysis was carried out on the CEL files using Transcriptomic Analysis Console (TAC) Affymetrix© software (4.0.1.36) and Transcripts ID’s were associated to human gene names, based on Chicken Ensemble