Quality-adjusted life years (QALYs) and disability-adjusted life years (DALYs) are summary health measures used in resource allocation decision making. However, the optimal choice of which summary measure to use in economic evaluations is unclear. On the basis of previously published literature, we attempt to clarify the use of summary health measures in cost-effectiveness analysis and recommend which summary measure to use for a given context. The selection of a summary health measure in cost-effectiveness analysis (CEA) depends to some extent on the philosophical background of the summary heath measures. Researchers may decide which measure to use based on the following selection criteria including but not limited to: 1) Purpose of research: DALYs are preferred for broader use in cost-effectiveness analysis, e.g., sectoral or generalized cost-effectiveness analysis. On the other hand, quality-adjusted life years (QALYs) are preferred for clinical decision making, evaluation of new clinical strategies, or program evaluation. 2) Norms: DALYs are preferably used in developing countries, whereas QALYs are the preferred outcome measure for conducting CEA in developed countries. 3) Availability of resources: The selection of a summary health measure is often driven by the availability of resources. Researchers in developing countries have limited resources in terms of funding to conduct CEAs using QALYs. On the other hand, disability weights representing population samples are easily accessible to researchers, which facilitate the use of DALYs as an outcome measure. The selection criteria for determining which summary health measure to use in CEA often overlap. The ultimate choice of summary measure should be based on the prioritization of goals and the availability of resources for the study.