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Background In collaboration with six European public health agencies as part of the PANDEM-2 consortium, we have developed and validated a self-assessment tool that captures the workforce capacities and capabilities needed at the institutional level within National Public Health Institutes (NPHIs) to deal with public health emergencies. Methods The work carried out in this study included (i) a review of existing tools for workforce assessment, (ii) focus group discussions and interviews to map the experiences and needs of NPHI's, (iii) the development of a tool for NPHI's to assess their workforce capacity and capabilities in public health emergency preparedness (PHEP) and (iv) refinement of the assessment tool via a Delphi study. Results Capacity markers were identified to assess the workforce required for PHEP functions and the availability of surge capacity during a public health emergency. The tool also enables NPHIs to analyze gaps in PHEP staff competencies. The assessment scores can assist NPHI pandemic preparedness by identifying and prioritizing training and recruitment needs. Conclusions In line with EU Regulation 2022/2371 on serious cross-border threats to health, article 11 Training of healthcare staff and public health staff, Member States (MS) are tasked with assessing current workforce capacity and capability gaps. The PANDEM-2 workforce self-assessment tool aligns with this requirement and will support effective planning and development to strengthen the public health workforce capacity in EU MS. [ABSTRACT FROM AUTHOR]