Genetically modified plants (GMPs) may soon be cultivated commercially in several member countries of the European Union (EU). According to EU Directive 2001/18/EC, post-market monitoring (PMM) for commercial GMP cultivation must be implemented, in order to detect and prevent adverse effects on human health and the environment. However, no general PMM strategies for GMP cultivation have been established so far. We present a conceptual framework for the design of environmental PMM for GMP cultivation based on current EU legislation and common risk analysis procedures. We have established a comprehensive structure of the GMP approval process, consisting of pre-market risk assessment (PMRA) as well as PMM. Both programs can be distinguished conceptually due to principles inherent to risk analysis procedures. The design of PMM programs should take into account the knowledge gained during approval for commercialization of a specific GMP and the decisions made in the environmental risk assessments (ERAs). PMM is composed of case-specific monitoring (CSM) and general surveillance. CSM focuses on anticipated effects of a specific GMP. Selection of case-specific indicators for detection of ecological exposure and effects, as well as definition of effect sizes, are important for CSM. General surveillance is designed to detect unanticipated effects on general safeguard subjects, such as natural resources, which must not be adversely affected by human activities like GMP cultivation. We have identified clear conceptual differences between CSM and general surveillance, and propose to adopt separate frameworks when developing either of the two programs. Common to both programs is the need to put a value on possible ecological effects of GMP cultivation. The structure of PMM presented here will be of assistance to industry, researchers, and regulators, when assessing GMPs during commercialization.