Chicken lines vary in susceptibility to diseases. During the breeding of broiler chickens most attention is given to economical important traits and no attention is given to the genes that are important in health. The use of antibiotics will be forbidden in the near future, therefore it is beneficial to breed chickens with a high resistance against diseases. The aim of this project is to reveal some of the genes and proteins involved in the resistance of broiler chickens, and to understand the gene-function relationships in intestinal health. First susceptibility to malabsorptie syndrome will be studied. It is known that different broiler lines differ in susceptibility for that disease. [Results:] A subtracted and normalised cDNA library was prepared specific for chicken intestine. This library was used to construct a cDNA microarray. Using the microarray genes were identified differing more than fourfold in expression between the susceptible and resistant broiler line after MAS induction. In the control situation no differences were found. Most identified genes were unknown in chicken. Homologues genes encode for proteins involved in food absorption, immunological functions or the function is not yet identified. For different genes the results with the quantitative RT-PCR confirmed the microarray data.