Transaction Cost Economics is a recent perspective to organizations analysis, and it is still little applied in the public sector. The purpose of this paper is to assess the relative efficiency of two primary health care platforms, one in Argentina and the another one in Brazil. The transaction costs are categorized, counted and normalized into quartiles from direct observation, interviews and documental review. Besides, institutional arrangements are described. The discriminating hypothesis of association between organizational efficiency and the alignment of transaction characteristics with the governance mode is comparatively tested. The analysis showed that the Brazilian case presented lower frequency of transaction costs because its institutional arrangement contains more coordination and incentives with less strategic uncertainty. The evaluation method developed in this paper highlights the importance of studying the characteristics of organization for the generation of knowledge and production of managerial contributions over public health service’s delivery.