Increasing volumes and speed of agricultural trade and the opening of new markets for agricultural products create greater challenges to systems established to protect countries from invasive organisms that can be harmful to human and animal health, crops and natural environments. In reaction to the threat of exotic pests and diseases, the World Trade Organization recognises the right of country members to protect themselves from the risks posed by exotic pests and diseases through the application of Sanitary and Phytosanitary (SPS) measures. One possible response from exporting countries facing SPS trade barriers is to obtain pest-free area (PFA) certification. While large benefits can potentially be achieved from greater access to world markets through the establishment and maintenance of a PFA, certification can be expensive. This paper aims to identify a theoretical framework on which to base the cost benefit analysis and the costs and benefits to be measured, from which a methodology for measuring costs and benefits may be developed. The literature relevant to analysing PFAs reveals that cost benefit analysis of the establishment of PFAs incorporate complex links between the economic aspects of this type of pest management and the biological characteristics of the pest or disease targeted and its environment.