Genetically modified (GM) crops have become a reality in our cropping system. The experiences with GM oilseed rape have shown that gene flow from a GM crop causes genetic contamination of non-GM crops and natural flora. This review summarizes technically available methods for gene flow assessment and proposes possible management methods. Methods for direct monitoring of gene flow include direct bioassay of plants and detection of phenotypic and molecular genetic markers contained in GM crops. A recent green fluorescent protein (GFP) marker technique can be powerful in monitoring gene flow as GFP inserted into a plant can be observed macroscopically under UV light. Appropriate analysis of data from direct assessment may give more useful information to mitigate gene flow. Observation with direct method provides real-time data and mathematical-statistical approaches may enable the long-term consequence to be predictable. Although an estimated gene flow is less than an acceptable level, gene flow must be maintained as low as possible with a systematic management. The management should be conducted stepwise; selection of gene flow-proof GM crops in the stage of development, risk assessment and regulation in the registration stage, cultural management, produce handling/transportation and a long-term monitoring in cropping stage. Promising methods for developing gene flow-proof GM crops include conferring cleistogamy and chloroplast transformation to mitigate pollen flow, and breeding non- or minimum shedding cultivars to mitigate seed dispersal. We strongly suggest that very high expression of a transgene or stacking multiple transgenes in the chloroplast could disturb the function of normal physiology, hence decreased performance of the GM crop. Before the approval of GM crops, proposed GM crops must go through the risk assessment. If the estimated risk of a GM crop exceeds an acceptable level, approval must be suspended. Once a GM crop is allowed for commercial release, additional efforts must follow, such as a continued long-term monitoring of the impact of GM crop cultivation, crop and herbicide rotations, GM crop-suited cultural practices, 'right-time' harvest, and all necessary gene flow-preventive practices. Such a systematic management incorporating various methods for the stages of GM crop utilization will minimize the risk of gene flow.