Bio-based fuels represent one of the most viable alternatives to petroleum-based fuel to meet transportation needs in the 21st century. The biofuel industry is in its infancy in Canada but shows considerable growth opportunity. The international interest in biofuels due to environmental and energy security concerns could result in a large and profitable export market for Canadian biofuel producers. Many industry participants are beginning to use biotechnology in their production processes to lower costs. Such use means they will be forced to contend with the unclear international regulation of trade in the products of biotechnology. Substantially different rules have been created by the Cartagena Protocol on Biosafety to the Convention on Biological Diversity, which governs only trade in biotechnology products, and the World Trade Organization, which governs trade in all goods. The inconsistencies of the regulatory situation create significant risks for biofuel producers, as their products may be blocked from important export markets.