New health technologies have made an impact in clinical and economic outcomes. Therefore, research methodologies that allow to evaluate the efficiency of these new technologies such as cost-effectiveness analysis are necessary. Cost-effectiveness analysis assess the value of health care interventions or drugs, the technology. Cost-effectiveness analysis is also deemed a determinant of modern health care practice, because the therapeutic options available at public (SUS) or private health care system must go through a formal health technology assessment in Brazil; thus, both the health care system and the health care professionals have to reevaluate the clinical consequences and costs of their actions to assure that the most efficient technologies are the one used in the practice. In this second article about health technology assessment we review the concepts of cost-effectiveness analysis, the steps involved in performing such analysis, and the criteria most frequently used to critically review the results.