Even with substantially increased attention to climate adaptation in developing countries in recent years, there are a number of important remaining research needs: better incorporating stakeholder input; using replicable methodologies to provide comparability across different settings; assuring that stakeholder input reflects the results of climate science, not simply perceptions; and effectively linking stakeholder input with the regional and national levels at which policy changes are made. This study reports the results of a methodology for identifying and prioritizing local, stakeholder-driven response options to climate change in agriculture. The approach is based on multi-criteria scoring methods previously applied to research planning and priority-setting in agricultural and natural resource management research, public health, and other areas. The methodology is a sequential approach built around needs assessments by local stakeholders; the incorporation of climate science results; the sharing of these results and climate adaption response options with stakeholders at a series of workshops; stakeholder priority-setting exercises using multi-criteria scoring; and validation with policymakers. The application is to three diverse agroecosystems in Mexico, Peru and Uruguay. Among the many findings is that, notwithstanding the wide diversity of agro-ecosystems, them are numerous similarities in the agricultural adaptation responses prioritized by local stakeholders. (C) 2014 Published by Elsevier Ltd.