Capacity is limited in the developing world to conduct cost-effectiveness analysis (CEA) of health interventions. In Thailand, there have been concerted efforts to promote evidence-based policy making, including the introduction of economic appraisals within health technology assessment (HTA). This paper reviews the experience of this lower middle-income country, with an emphasis on the creation of the Health Intervention and Technology Assessment Program (HITAP), including its mission, management structures and activities. Over the past 3 decades, several HTA programmes were implemented in Thailand but not sustained or developed further into a national institute. As a response to increasing demands for HTA evidence including CEA information, the HITAP was created in 2007 as an affiliate unit of a semi-autonomous research arm of the Ministry of Public Health. An advantage of this HTA programme over previous initiatives was that it was hosted by a research institute with long-term experience in conducting health systems and policy research and capacity building of its research staff, and excellent research and policy networks. To deal with existing impediments to conducting health economics research, the main strategies of the HITAP were carefully devised to include not only capacity strengthening of its researchers and administrative staff, but also the development of essential elements for the country's health economic evaluation methodology. These included, for example, methodological guidelines, standard protocols and benchmarks for resource allocation, many of which have been adopted by national policy-making bodies including the three major public health insurance plans. Networks and collaborations with domestic and foreign institutes have been sought as a means of resource mobilization and exchange. Although the HITAP is well financed by a number of government agencies and international organizations, the programme is vulnerable to shortages of qualified research staff, as most staff work on a part-time or temporary basis. To enhance the utilization of its research findings by policy makers, practitioners and consumers, the HITAP has adopted the principles of technical excellence, policy relevance, transparency, effective communication and participation of key stakeholders. These principles have been translated into good practice at every step of HTA management. In 2007 and 2008, the HITAP carried out assessments of a wide range of health products, medical procedures and public health initiatives. Although CEA and other economic evaluation approaches were employed in these studies, the tools and underlying efficiency goal were considered inadequate to provide complete information for prioritization. As suggested by official stakeholders, some of the projects investigated broader issues of management, feasibility, performance and socio-political implications of interventions. As yet, it is unclear what role HITAP research and associated recommendations have played in policy decisions. It is hoped that the lessons drawn on the creation of the HITAP and its experience during the first 2 years, as well as information on its main strategies and management structures, may be helpful for other resource-constrained countries when considering how best to strengthen their capacity to conduct economic appraisals of health technologies and interventions.