Often the limits of detection of genetically engineered organisms (GEOs, LMOs, GMOs) determine what legislation sets as thresholds of allowable contamination of the human food chain with GEOs. Many countries have legislation that is triggered by certain thresholds of contamination. Importantly, international trade in food and animal feed is becoming increasingly vulnerable to interruptions caused by the ambiguity GEOs can create when shipments are monitored at the border. We examine the tools available for detection. Four key error-generating stages are identified with the aim of prompting a higher uniform standard of routine analysis at export and import points. Contamination of the New Zealand corn crop with GEOs is used as a case study for the application of monitoring tools and vulnerability to errors. These tools fail to meet emerging food safety requirements, but some improvements are in development.