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This study outlines the ways in which different health technology assessment (HTA) organizations deal with uncertainty in relative effectiveness assessments (REAs), using the GRADE framework as a common reference. Guidelines regarding REA and uncertainty assessment methods and three most recent HTA reports (as of April 2020) of seven HTA organizations in Germany, England and Wales, France, the Netherlands, Europe (EUnetHTA), the USA, and Canada were included. First, it was analyzed how each organization addressed uncertainty on the following levels of evidence: (i) individual studies, (ii) body of evidence for one outcome, (iii) body of evidence across all outcomes, and (iv) added net benefit. Second, the extent to which HTA organizations considered the eight domains of certainty of evidence defined by GRADE was assessed. For individual studies, checklists were the most common approach to express uncertainty (4/7 organizations). Uncertainty in the body of evidence for all outcomes and in added benefit was combined in a single conclusion by five organizations. All organizations reported on at least 4/5 downgrading domains of GRADE, while the three upgrading domains were reported less. The operationalization of the assessment of multiple domains was unclear due to vague or absent guidelines. HTA organizations consider most domains of the GRADE framework, but approaches to assess uncertainty within REAs on different levels of evidence differ substantially between organizations. More alignment and guidance on the best methods to deal with uncertainty within HTA could lead to more clarity for stakeholders and to more aligned reimbursement recommendations.