The Gene Technology Regulator's approval of Bayer CropScience's genetically modified (GM) canola variety, InVigor, and Monsanto's Roundup Ready, means that the commercial planting of Australia's first GM food crop is imminent. Under such circumstances, for Australia to continue marketing non-GM canola and comply with worldwide labelling requirements segregation must be implemented. This study investigates the cost effectiveness of three possible segregation methods. In considering each of these methods the increase in total grain handling cost due to segregation is expected to be between 5 and 9 per cent, or $1.35/tonne and $2.70/tonne. Such an increase is comparable with segregation costs reported in current Canadian literature.