This paper outlines a six-country study of institutionalised forms of HIV/AIDS-related discrimination in the Asia-Pacific region. Although recognised as a barrier to disease prevention and treatment, very limited data are available on the effects of institutionalised HIV-related stigma and discrimination. Understanding the forms of discrimination within the institutions where they occur is the first step to identifying effective ways of promoting compassionate, non-discriminatory treatment of PLWHA. Thus, the goal of this research project was to document institutional discrimination against PLWHA, as guided by the UNAIDS Protocol for the Identification of Discrimination Against People Living with HIV (2000), in six Asian countries: India, Thailand, Philippines, China, Vietnam and Indonesia. As a precursor to the six individual studies, this paper provides a brief overview of the literature on HIV discrimination, and then describes the UNAIDS Protocol and the shared methodological considerations relevant to all of the study sites. Commonalities in sampling, procedures and analysis are also discussed.