Since its independence was restored in 1991, Estonia has restructured its public health and health security landscape, and joined the European Union (EU) in 2004. Since this, and despite its relatively small geographical size and population, the country's economic growth and the importance of Estonia and Estonians in the development of the information and communication technology (ICT) sector has been much remarked upon. This has brought about interest in the development and uptake of ICT solutions within the health sector, and considerable upgrades to health provision and infrastructure. Due to Estonia's geographical position, health security will always be of significant interest to the country and much has been achieved in the last 20 years. With this combination of factors, the WHO Joint External Evaluation (JEE) in Estonia was deemed of interest not only to Estonia but also as an example of how a small, now highly developed country can work to improve its health security. A further point of interest is that Estonia has, in general, a widely spaced population with low density; another challenge to providing services which needs to be overcome. During the JEE mission to Estonia, capacities in 19 technical areas were evaluated through a peer-to-peer collaborative process that brought subject matter experts together with members of the external assessment team. The team was composed of representatives from 10 Member States, international organizations or academic institutions, engaged in a week-long series of technical discussions and on-site visits. The primary objective of the assessment was to compile a comprehensive array of evidence, encapsulating evaluations, reviews and other relevant insights. The aim was to equip Estonian authorities with actionable information for improving implementation of the International Health Regulations (IHR) 2005, encompassing cost estimates, high-level commitment and accountability. While the assessment itself can facilitate knowledge exchange and networking, it does not improve health security capacities per se. Therefore, identified priority recommendations should be captured in a National Action Plan for Health Security (NAPHS), which in turn drives translation of priorities into concrete technical activities. The external team acknowledges that many recommendations deal with establishing committees, action plans and strategies, all of which may be crucial steps for capacity development, but nevertheless need to be streamlined given constraints on human resource capacity.