The government of Uganda is currently testing the performance of genetically modified (GM) cotton varieties. Cotton is cultivated in Uganda for two main reasons: 1) agro-ecological conditions favor cotton cultivation, and 2) there is a long tradition of cotton cultivation in the country. Two main research questions are addressed in this study: a) would the adoption of genetically modified (GM) cotton benefit Ugandan farmers? b) Would the use of GM seed be more profitable than the low input traditional system or than the organic production system? Stochastic budget analysis is used to address these questions. The results show that estimated values of cotton profitability do not seem to justify the investment in a complex technology. The question then is how transferable is GM technology and how easily can it be adopted by Ugandan farmers. The vertical integration of the chain could facilitate the dissemination of the technology, but availability of seed and inputs of good quality and appropriate extension support have to be guaranteed.