A workshop organized by the International Life Sciences Institute (ILSI) Research Foundation, ILSI Brasil, and Brazilian Agricultural Research Corporation (EMBRAPA) brought together scientists from government, industry and academia to explore problem formulation for environmental risk assessment (ERA) of genetically modified crops. The workshop focused on the application of current scientific knowledge related to the ERA of GM crops in the Brazilian context of the National Biosafety Technical Commission (CTNBio) Normative Resolution #05 requirements and the local environment. Due to the importance of cotton and sugarcane to Brazil’s economy and the potential environmental impacts associated with introducing genetically modified varieties, these crops were used as case studies to illustrate and discuss the general concepts in problem formulation. This report is a summary of the discussions from this workshop.