Abstract: The maintenance of biodiversity of organisms, especially microbes in the soil, plays a key role for a healthy and sustainable agroecosystem. Agricultural activities including farming systemsaffect significantly the structure and ecological functions of soil-borne plant-associated microorganisms. As a new biotic component of the ecosystem, released genetically engineered crops initiate a change in the biotic community, the health and the stability of an agricultural ecosystem. This paper focuses on the behavior of gene products released from the roots of transgenic pest and disease-resistant crops (TPDRC) and the decomposition of TPDRC residue, and their effects on various organisms in the rhizosphere and surrounding crop residues in the soil. It is concluded that gene expression products have a long-term effect and lead to complex changes. It is suggested that a long-term study on ecological impacts of various released TPDRC is necessary. The emphasis should be focused on the following three aspects: (1) behavior of various products from different transgenic plants and their biotic activity in agroecosystems; (2) influence of transgenic plants on community composition of soil borne microorganisms and (3) influence of various isolated and purified gene expression products on microorganism functional groups in container culture conditions.