Electronic health services have been received with a tremendous interest world over. Patients consider hospital websites as highly important sources for health information and services. As a number of health institutes are carrying out projects to improve their websites, the need to design proper assessment means to measure whether they have achieved or are going to achieve their targets arises. Proper assessment of these websites gives us crucial information on the kind of changes needed to make them successful. To satisfy this need, an instrument called Health Sector Website Assessment Index (HSWAI) was developed, integrating the assessment of content, services, community interaction and technology features criteria, under a multi-indicator approach. Many of the considered indicators could be used to monitor progress towards the achievement of Sustainable Development Goal (SDG) 3, which is the United Nations health-focused goal. The purpose of this study is to highlight the challenges of developing and applying the assessment instrument for health institute websites. The paper covers key issues and challenges in conceiving, designing, developing, refining and validating HSWAI, and finally in applying it to a set of Portuguese health institutes. The results of this study could provide several insights and recommendations to e-Government assessment researchers and practitioners at the national and agency levels on the development of relative e-Government assessment tools. Studies such as the current one, apart from presenting applied solutions and relative lessons learned, are valuable to the conceptualization and application of present and future e-Government assessment initiatives, regardless of the sector where the effort occurs. Copyright © 2022. Published by Elsevier Ltd.