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Abstract Background Most patients with alcohol use disorders (AUDs) never receive alcohol treatment, and experts have recommended management of AUDs in primary care. The Choosing Healthier Drinking Options In primary CarE (CHOICE) trial was a randomized controlled effectiveness trial of a novel intervention for primary care patients at high risk for AUDs. This report describes the conceptual and scientific foundation of the CHOICE model of care, critical elements of the CHOICE trial design consistent with the Template for Intervention Description and Replication (TIDieR), results of recruitment, and baseline characteristics of the enrolled sample. Methods The CHOICE intervention is a multi-contact, extended counseling intervention, based on the Chronic Care Model, shared decision-making, motivational interviewing, and evidence-based options for managing AUDs, designed to be practical in primary care. Outpatients who received care at 3 Veterans Affairs primary care sites in the Pacific Northwest and reported frequent heavy drinking (≥4 drinks/day for women; ≥5 for men) were recruited (2011–2014) into a trial in which half of the participants would be offered additional alcohol-related care from a nurse. CHOICE nurses offered 12 months of patient-centered care, including proactive outreach and engagement, repeated brief motivational interventions, monitoring with and without alcohol biomarkers, medications for AUDs, and/or specialty alcohol treatment as appropriate and per patient preference. A CHOICE nurse practitioner was available to prescribe medications for AUDs. Results A total of 304 patients consented to participate in the CHOICE trial. Among consenting participants, 90% were men, the mean age was 51 (range 22–75), and most met DSM-IV criteria for alcohol abuse (14%) or dependence (59%). Many participants also screened positive for tobacco use (44%), depression (45%), anxiety disorders (30-41%) and non-tobacco drug use disorders (19%). At baseline, participants had a median AUDIT score of 18 [Interquartile range (IQR) 14–24] and a median readiness to change drinking score of 5 (IQR 2.75–6.25) on a 1–10 Likert scale. Conclusion The CHOICE trial tested a patient-centered intervention for AUDs and recruited primary care patients at high risk for AUDs, with a spectrum of severity, co-morbidity, and readiness to change drinking. Trial registration The trial is registered at clinicaltrial.gov (NCT01400581).