Transgenic crops are being deployed at increasing rates in agricultural landscapes worldwide. This leads to increasing genetic uniformity of agroecosystems and enhances farmers dependence on biotechnological innovations subject to proprietary regimes controlled by multinational corporations. As developed transgenic crops respond to market niches and opportunities, there has been little consideration of the ecological implications of their deployment. Existing ecological theory and emerging research data suggest that the massive planting of transgenic monocultures can create critical environmental impacts ranging from gene flow between transgenic crops and wild relatives, the creation of super-weeds and the rapid development of insect resistance, to impacts on soil fauna and nontarget organisms. The consequences of such effects on agroecosystem health are analyzed are herein.