To determine where, when, and how to increase yields, researchers often analyze the yield gap (Yg), the difference between actual current farm yields and crop yield potential. Crop yield potential (Yp) is the yield of a crop cultivar grown under specific management limited only by temperature and solar radiation and also by precipitation for water limited yield potential (Yw). Yp and Yw are critical components of Yg estimations, but are very difficult to quantify, especially at larger scales because management data and especially daily weather data are scarce. A protocol was developed to estimate Yp and Yw at national scales using site-specific weather, soils and management data. Protocol procedures and inputs were evaluated to determine how to improve accuracy of Yp, Yw and Yg estimates. The protocol was also used to evaluate raw, site-specific and gridded weather database sources for use in simulations of Yp or Yw. The protocol was applied to estimate crop Yp in US irrigated maize and Chinese irrigated rice and Yw in US rainfed maize and German rainfed wheat. These crops and countries account for \u3e20% of global cereal production. The results have significant implications for past and future studies of Yp, Yw and Yg. Accuracy of national long-term average Yp and Yw estimates was significantly improved if (i) \u3e 7 years of simulations were performed for irrigated and \u3e 15 years for rainfed sites, (ii) \u3e 40% of nationally harvested area was within 100 km of all simulation sites, (iii) observed weather data coupled with satellite derived solar radiation data were used in simulations, and (iv) planting and harvesting dates were specified within ± 7 days of farmers actual practices. These are much higher standards than have been applied in national estimates of Yp and Yw and this protocol is a substantial step in making such estimates more transparent, robust, and straightforward. Finally, this protocol may be a useful tool for understanding yield trends and directing research and development efforts aimed at providing for a secure and stable future food supply