Chicken lines differ in genetic disease susceptibility. The scope of the research described in this thesis was to identify genes involved in genetic disease resistance in the chicken intestine. Therefore gene expression in the jejunum was investigated using a microarray approach. An intestine specific cDNA microarray was generated from a normalized and subtracted library. Gene expression in young chickens was studied using two different disease models, malabsorption syndrome and Salmonella enteritidis . For each model two different chicken lines were studied, which differed in susceptibility to the specific diseases. Gene expression differences between the chicken lines were found under control and under infected conditions. In the studies described here the main focus was on genes that could be involved in disease susceptibility. Large differences between the chicken lines with different genetic backgrounds were found in their gene expression responses to the infections. After malabsorption syndrome the more susceptible chicken line regulated immune related genes, genes involved in food absorption and genes with unknown functions. The chicken line most susceptible for salmonella upregulated genes involved in inflammation, or with unknown functions, whereas the more resistant chicken line regulated genes involved in acute phase response, the fibrinogen system, actin polymerisation, and also genes with unknown functions. Most gene expression responses to both infection models were found 1 day post infection. Gene expression differences between the two chicken lines lead to the hypothesis that immunological differences could be the basis of differences in susceptibility for Salmonella . Therefore the two chicken lines were studied for the phagocytic properties of intestinal mononuclear cells and these properties were different for the two chicken lines. Also, a decrease in the number of CD4 + T-cells and macrophages in response to the Salmonella infection was found only in one chicken line. In both chicken lines the number of CD8 + T-cells increased, but faster in the susceptible chicken line. So genetic background influences intestinal gene expression responses and immunological responses.