There is a growing body of literature about the impacts of Bacillus thuringiensis (Bt) cotton in developing countries. While many studies show remarkable benefits for farmers, there are also reports that question these results. Most previous studies consider impacts in deterministic terms, neglecting existing variability. Here we explain the main factors influencing the agronomic and economic outcomes. Apart from differences in pest pressure and patterns of pesticide use, germplasm effects can play an important role. Theoretical arguments are supported by empirical evidence from India. Better understanding of impact variability can help explain some of the paradoxes in the recent controversy over genetically modified crops. Copyright 2006, Oxford University Press.