Agricultural productivity and the environmental impacts of agriculture are most effectively managed using procedures that are based on sound ecological thinking.  Monitoring procedures for genetically modified (GM) crops that are now a part of international protocols and postmarket requirements should be developed to protect the productivity and ecological integrity of farming systems.  Risk assessment procedures are in development, and monitoring must compensate for deficiencies that will only be rectified through field experience in GM commodities.  The history of monitoring in agriculture tells us that even clearly adverse impacts of GM cropping will be difficult to detect because of the inherent complexity and heterogeneity of farming systems.  Ecosystem-level indicators are relevant (e.g., those employed in PAGE and MEA), as well as crop-specific indicators, and their relative contribution is dependent upon the specific farming-system context.  Long-term monitoring has made positive contributions to the retrospective analysis of trends associated with production and off-crop impacts in agriculture.  Globally, farming systems differ significantly in the forms of monitoring that are required to protect them.  This is because of differences between crops and cropping practices, differences in underlying ecological processes and climate, differences in the distribution of knowledge among growers and researchers, differences in policy and regulatory environments and the degree of feedback to agricultural change and differences in the quality and availability of relevant monitoring data.  All monitoring programmes for GM crops should be designed in such a way that their potential value is clear, and in ways that will result ultimately in effective management.  They should provide a clear and rigorous explanation for the selection of indicators, including a sampling design that meets the requirements for statistical power.  Critically, there should be a clear connection between the results of monitoring and decision-making.