Estimates of climate change impacts are often characterized by large uncertainties that reflect ignorance of many physical, biological, and socio-economic processes, and which hamper efforts to anticipate and adapt to climate change. A key to reducing these uncertainties is improved understanding of the relative contributions of individual factors. We evaluated uncertainties for projections of climate change impacts on crop production for 94 crop–region combinations that account for the bulk of calories consumed by malnourished populations. Specifically, we focused on the relative contributions of four factors: climate model projections of future temperature and precipitation, and the sensitivities of crops to temperature and precipitation changes. Surprisingly, uncertainties related to temperature represented a greater contribution to climate change impact uncertainty than those related to precipitation for most crops and regions, and in particular the sensitivity of crop yields to temperature was a critical source of uncertainty. These findings occurred despite rainfall’s important contribution to year-to-year variability in crop yields and large disagreements among global climate models over the direction of future regional rainfall changes, and reflect the large magnitude of future warming relative to historical variability. We conclude that progress in understanding crop responses to temperature and the magnitude of regional temperature changes are two of the most important needs for climate change impact assessments and adaptation efforts for agriculture.