Genetically modified crops are the topic of a controversial debate. While some believe they have the potential to address many of the world s most challenging, interrelated problems, others mainly point to the risks, uncertainty and to some socio-economic issues. In this perspective a lot of research has been done on the agronomic and economic performance, on the effects on human health and the environmental risks and on stakeholders attitudes. Given that farmers, as actual potential producers of these crops play a crucial role in their eventual success surprisingly little attention has gone to their preferences. This paper focuses on farmers in Burkina Faso and uses two choice experiments to evaluate the preferences for two types of GM innovations: Bt cotton, which is a first generation GM crop, in which the focus is on input traits and biofortified sorghum, a second generation GM crop with a focus on output traits. Results show that farmers have a clear interest in pest resistance, and are quite satisfied with the current configuration of the Bt cotton crop. Moreover farmers are very open to the addition of micronutrients to the sorghum. This is an important finding in the context of the African Biofortified Sorghum initiative Acknowledgement :