The study was conducted to evaluate the adequacy of expression profiling for the characterization of potential physiological side effects of genetically modified (GM) feed components. Feeding experiments with rats fed either GM or non-GM feed components were conducted and a comparative expression profiling, using DNA-chip-technology, was done. As a prerequisite for these expression studies data analysis parameters were optimized. Diet-associated expression differences between the two feeding groups were observed in spleen, small intestine and liver. It was shown that expression profiling provides great sensitivity in monitoring physiological reactions of an organism to such diets.