Genetically engineered transgenic crop varieties (TGVs) have spread rapidly in the last 10 years, increasingly to traditionally-based agricultural systems (TBAS) of the Third World both as seed and food. Proponents claim they are key to reducing hunger and negative environmental impacts of agriculture. Opponents claim they will have the opposite effect. The risk management process (RMP) is the primary way in which TGVs are regulated in the US (and many other industrial countries), and proponents claim that the findings of that process in the US and its regulatory consequences should be extended to TBAS. However, TBAS differ in important ways from industrial agriculture, so TGVs could have different effects in TBAS, and farmers there may evaluate risks and benefits differently. To evaluate some potential impacts of TGVs in TBAS we used the RMP as a framework for the case of Bt maize in Mesoamerica and Cuba. We interviewed 334 farmers in Cuba, Guatemala and Mexico about farming practices, evaluations of potential harm via hypothetical scenarios, and ranking of maize types. Results suggest high potential for transgene flow via seed, grain and pollen; differences in effects of this exposure in TBAS compared with industrial agriculture; farmers see some potential consequences as harmful. Perceptions of harm differ among farmers in ways determined by their farming systems, and are different from those commonly assumed in industrial systems. An RMP including participation of farmers and characteristics of TBAS critical for their functioning is necessary to ensure that investments in agricultural technologies will improve, not compromise these agricultural systems.