This study aims to analyze the effects of corn segregation on Brazilian transport and storage logistics, and how it impacts global competitiveness. A partial equilibrium model as a Mixed Complementarity Problem (MCP) was developed to guide the implementation of more effective policies and support new investments. The Cartagena Protocol on Biosafety requirements affects the logistics of transport and storage in Brazil. Intermodal flows were most affected and significant commercial reductions occurred in the regions farthest from export ports. This research is original in its use of a model and forecast scenarios to measure how biotechnology regulatory issues directly affect infrastructure logistics. Establishing stringent identity preservation systems affects these projects, since intermodal flows are most affected by such systems.