Knowledge and information relating to international trade agreements and their implications during the past 17 years, both within and external to Thailand. To reveal the implications and impact systematically, the conceptual framework for analysis was drafted and the implications were mapped along the medicine value chain. The mapping shows cross-link of the implications and took concerns of health sectors. Focusing on medicines, despite of positive impact, international trade agreements have had significant negative impacts on the Thai medicine system. There is worldwide recognition that expensive prices and higher expenditure of medicines result from the Agreement on Trade-Related Aspects of Intellectual Property Rights (TRIPS); this research identified further implications including: the opening up of market access to government procurement and limitations on policy space for medicine management systems as well as public health. This paper also demonstrates the experiences of Thailand, India and Malaysia regarding TRIPS flexibilities. It was shown that all three countries exercised “other use without authorization of the right holder”, which is a TRIPS flexibility, to strike the balance between individual right and obligation in access to affordable essential medicines, although difficulties and consequences were found in the process of exercising this right. Evidence shows that Thailand, as a developing country, may support the voluntary license but must keep all TRIPS flexibilities, including the compulsory license, as tool to overcome barriers to access and ensure the human right to health. Further system research as well as investigation of cross-country impact of FTAs in and among ASEAN members are recommended.