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Introduction: Despite calls for screening tools to help providers monitor long-term opioid therapy (LTOT) harms, and identify patients likely to experience harms of discontinuation, such screening tools do not yet exist. Current assessment tools are infeasible to use routinely in primary care and focus mainly on behaviours suggestive of opioid use disorder to the exclusion of other potential harms. This paper describes a study protocol to develop two screening tools that comprise one integrated instrument, S creen to E valuate and T reat (SET). SET1 will indicate if LTOT may be harmful to continue (yes or no), and SET2 will indicate if tapering to discontinue opioids may be harmful to initiate (yes or no). Patients receiving LTOT who screen positive on the SET tools should receive subsequent additional assessment. SET will give providers methods that are feasible to implement routinely to facilitate more intensive and comprehensive monitoring of patients on LTOT and decision-making about discontinuation., Methods and Analysis: We will develop the screening tools, SET1 and SET2, concurrently. Tool development will be done in stages: (1) comprehensive literature searches to yield an initial item pool for domains covered by each screening tool; (2) qualitative item analyses using interviews, expert review and cognitive interviewing, with subsequent item revision, to yield draft versions of each tool; and (3) field testing of the draft screening tools to assess internal consistency, test-retest reliability and convergent and discriminant validity., Ethics and Dissemination: Ethical approval was obtained from the Institutional Review Boards of Stanford University and the University of California, San Francisco for the VA Palo Alto Health Care System, and the VA San Francisco Healthcare System, respectively. Findings will be disseminated through peer-reviewed manuscripts and presentations at research conferences., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2021. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)