This manual is part of Task 3.1 in Work Package 3 (WP) of the Population Health Information Research Infrastructure (PHIRI). In this task, (virtual) country visits are carried out to map the state of play of European countries’ health information (HI) systems that monitor the wider effects of COVID-19 on population health. A HI system assessment tool has been developed by WHO Europe through the European Health Information Initiative, EHII (WHO Regional Office for Europe, 2021). The tool was adapted to accommodate the COVID-19 perspective. The mapping includes an assessment of the underlying needs and how these relate to current gaps in the European HI systems. Additionally, it investigates potential future needs and gaps to which PHIRI can respond through its services. This document is the PHIRI COVID-19 HIS assessment manual. It defines the objectives of the HIS assessment and how the assessment process is organized. It provides guidelines for the execution of the assessments and describes the roles and tasks of the different types of experts involved.