Campylobacter jejuni colonises the caecum of more than 90% of commercial chickens. Even though colonisation is asymptomatic, we hypothesised that it is mediated by activation of several biological pathways. We therefore used chicken-specific 20K oligonucleotide microarrays to examine global gene expression in C. jejuni-challenged birds. Microarray results demonstrate small but significant fold-changes in expression of 270 genes 20 h post-challenge, corresponding to a wide range of biological processes including cell growth, nutrient metabolism and immunological activity. Expression of NOX1 (2.3-fold) and VCAM1 (1.5-fold) were significantly increased in colonised birds ( P < 0.05), indicating oxidative burst and endothelial cell activation, respectively. Microarray results, supplemented by qRT-PCR analyses demonstrated increased TOPK (1.9-fold), IL17 (3.6-fold), IL21 (2.1-fold), IL7R (4-fold) and CTLA4 (2.5-fold) gene expression ( P < 0.05), which was suggestive of T cell mediated activity. Combined these results suggest that C. jejuni has nominal effects on global caecal gene expression in the chicken but significant changes detected are suggestive of a protective intestinal T cell response.