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Abstract Background Pragmatic trials provide the opportunity to study the effectiveness of health interventions to improve care in real-world settings. However, use of open-cohort designs with patients becoming eligible after randomization and reliance on electronic health records (EHRs) to identify participants may lead to a form of selection bias referred to as identification bias. This bias can occur when individuals identified as a result of the treatment group assignment are included in analyses. Methods To demonstrate the importance of identification bias and how it can be addressed, we consider a motivating case study, the PRimary care Opioid Use Disorders treatment (PROUD) Trial. PROUD is an ongoing pragmatic, cluster-randomized implementation trial in six health systems to evaluate a program for increasing medication treatment of opioid use disorders (OUDs). A main study objective is to evaluate whether the PROUD intervention decreases acute care utilization among patients with OUD (effectiveness aim). Identification bias is a particular concern, because OUD is underdiagnosed in the EHR at baseline, and because the intervention is expected to increase OUD diagnosis among current patients and attract new patients with OUD to the intervention site. We propose a framework for addressing this source of bias in the statistical design and analysis. Results The statistical design sought to balance the competing goals of fully capturing intervention effects and mitigating identification bias, while maximizing power. For the primary analysis of the effectiveness aim, identification bias was avoided by defining the study sample using pre-randomization data (pre-trial modeling demonstrated that the optimal approach was to use individuals with a prior OUD diagnosis). To expand generalizability of study findings, secondary analyses were planned that also included patients newly diagnosed post-randomization, with analytic methods to account for identification bias. Conclusion As more studies seek to leverage existing data sources, such as EHRs, to make clinical trials more affordable and generalizable and to apply novel open-cohort study designs, the potential for identification bias is likely to become increasingly common. This case study highlights how this bias can be addressed in the statistical study design and analysis. Trial registration ClinicalTrials.gov , NCT03407638 . Registered on 23 January 2018.