Transgenic biotechnology and its products provide important solutions for the great challenge of global food security. Biosafety assessment of genetically modified organisms (GMOs) including their food and environmental safety is a prerequisite for the commercialization and safe application of transgenic biotechnology products. However, existing methodologies cannot meet the urgent requirements for rapid biosafety assessment of the increasing number of new and sophisticated GMOs. Therefore, a new, more efficient and objective biosafety assessment methodology is needed. The decision tree, a widely used methodology for data mining and analysis, has a particular function in solving complicated problems. This article introduces the concepts, characteristics, and categorization of a decision tree, as well as methods for decision tree construction. Our objective is to explore the potential of establishing a diagnostic platform for biosafety assessment of GMOs in an efficient and accurate way. This biosafety assessment platform should also be useful for predicting the safety of the new generation of GMOs, and for educating the public on environmental biosafety, thereby providing a solid base for further development of transgenic technology and safe application of transgenic products.