This article seeks to highlight some potential indicators and benchmarks for the right to health under the International Covenant on Economic, Social and Cultural Rights, ratified by Estonia. These potential key indicators, as part of a human rights based approach to health indicators being developed by the UN Special Rapporteur, are argued to be particularly important in the context of the exceptionally high HIV rates among the Russian speaking population in Estonia. The historical emergence of the HIV epidemic in Estonia is traced, comparing its development with the situations in Latvia and Lithuania. This article describes the current extent of the HIV epidemic in Estonia which is the country with the highest reported number of HIV infections per capita in Europe, a number impacting in an extremely disproportionate fashion on its Russian-speaking population, particularly in North-Eastern Estonia. Understanding of the HIV epidemic in Estonia cannot exclude the social contextual factors of the social marginalization of many among the Russian-speaking population, the ‹alien’ status of those without citizenship of Estonia or any other State, and other failures of Estonian State policy with regard to intravenous drug use and HIV in the recent past. HIV among the prison population is also examined as disproportionately impacting upon Russian-speaking prisoners. It is argued that the language and logic of the Estonian State Integration Programme, as well as Estonia’s Second Report on the implementation of the Council of Europe Framework Convention for the Protection of National Minorities (2004) which refer to its Russian-speaking citizens as ‹non-Estonians’ is discrimination based on ethnic origin. In order to develop a system of State accountability in relation to the right to health, candidate indicators and benchmarks are proposed as structural, process and outcome indicators relevant to Estonia regarding the right to health and HIV, intravenous drug use, socio-economic integration and its Russian-speaking population.