While a fierce debate about the advantages and disadvantages of genetically modified crops is ongoing, it is surprising that farmers are often not consulted. In Burkina Faso, where insect resistant Bollgard II® cotton (further termed Bt cotton) was commercially released in 2008, studies highlight that cotton producers are in general satisfied with the reduction in insecticide use while the economic benefits are a source of controversy. To gain insight into farmers’ preferences towards attributes in cotton cultivation, a discrete choice experiment (DCE) was developed. Five key attributes were identified to describe improved cotton varieties: seed development and provenance, seed costs, yield, required number of insecticide sprays, and preservation of agricultural practices. Farm-gate surveys were conducted among 324 cotton farmers in Western Burkina Faso. The results show that overall, farmers have a positive preference towards yield improvements and a negative preference towards pure private seed development and towards an increase in the requested number of insecticide applications or in the seed costs. According to their varieties at the time of the surveys (Bt and non-Bt), a difference was observed regarding their preferences for a status quo situation, indicating that those growing Bt had a stronger preference to keep the status quo than non-Bt farmers. When dividing the sample in segments based on the farm size, it was shown that there were different preferences with respect to the development of the variety and the required number of insecticide applications. Overall, it can be concluded from this study that economic benefits (linked to higher yields, lower seed costs, or reduced pesticide use) shape farmer’s preferences.