The expression levels of two marker proteins (phosphinotrichin acetyltransferase, PAT and wheat germ agglutinin, WGA) in the transgenic wheat lines and their resistance to digestion in small intestine of rats were studied in comparison with their non-transgenic counterpart obtained from green house and field experiments of two subsequent years. The marker proteins were quantified by ELISA. It was found that the expression of PAT and WGA markedly increased when the wheat was grown in the field compared to that in the greenhouse. There were no significant differences between the WGA contents of the parent and transgenic wheat lines, but a broad range of expression of PAT and WGA was observed in the transgenic lines. PAT did not survive in the small intestine of the rats, while WGA was resistant to digestion in different ratios and was bound to the intestinal epithelium.