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Abstract This article explores the issue of designing government institutions in charge of the climate agenda in the Latin American context. To this end, it identifies some key political challenges facing climate institutions in the countries of the region. In particular, it discusses four topics: First, the cross cutting nature of the climate agenda; second, the long-term perspective (and levels of uncertainty) posed by climate problems against the tighter time frames of political cycles; third, the power asymmetry between the government agencies in charge of climate issues and other areas of government; finally, the implementation deficits of climate policies. The article also discusses different types of institutional design responses to address each of these challenges and the advantages and limitations of each one.