Background Worldwide, there is a need for formalization of the priority setting processes in health. Recent research has used the term multicriteria decision analysis for methods that systematically include preferences for both equity and efficiency. The present study compares decision-makers' preferences at the country level for a set of equity and efficiency criteria according to a multicriteria decision analysis framework. Methods Discrete choice experiments were conducted for Brazil, Cuba, Nepal, Norway, and Uganda. By using standardized methods, we elicited preferences for intervention attributes using a individual choice questionnaire. A multinomial logistic regression was applied to estimate the coefficients for all single-policy criteria, per country. Attributes were assigned to an equity group or to an efficiency group. After testing for scale variance, predicted probabilities for interventions with both types of attributes were compared across countries. Results The Norway and Nepal groups showed considerable preferences for efficiency criteria over equity criteria with percent change in respective predicted sum probabilities of [10%, −84%] and [6%, −79%]. Brazil and Uganda also showed preference for the efficiency criteria though less convincingly ([−34%, −93%], [−18%, −63%], respectively). The Cuban group showed the strongest preferences with equity attributes dominating efficiency ([−52%, 213%]). Conclusions Group preferences of policymakers show explicit but varying trade-offs of efficiency and equity in these diverse settings. This multicriteria decision analysis approach, using discrete choice experiments, indicates that systematic setting of health priorities is possible across a variety of countries. It may be a valuable tool to guide health reform initiatives.