The purpose of this study is to evaluate the efficacy of repetitive transcranial magnetic stimulation (rTMS) as a treatment for Veterans with an alcohol use disorder (AUD) to decrease the exceedingly high rate of relapse associated with this condition. At least 60% of those with AUD will experience a major relapse period within 6 months of treatment, irrespective of the intervention (psychosocial and/or pharmacological) employed. Consequently, the high prevalence of AUD and relapse following treatment in Veterans is associated with substantial resource allocation and costs for the DVA Health Care System. Current pharmacological and psychosocial interventions demonstrate only a moderate level of efficacy, which is reflected in the high rate of relapse in AUD. rTMS is a neurostimulation method that is at the forefront of innovative, non-invasive, and safe treatments for AUD, and the disorders that commonly co-occur with AUD. To reduce the high rate of relapse in Veterans with AUD, it is necessary for interventions to more effectively address the associated neurobiological dysfunction and salient co-occurring conditions. Accordingly, additional rigorously controlled studies are required to determine if rTMS is an effective treatment for Veterans with AUD. Participants will be recruited from VA Palo Alto Health Care System (VAPAHCS) residential substance abuse treatment clinics A double-blind randomized clinical trial with two groups: Active rTMS Treatment Group (Active rTMS) – will receive four to five treatments (two treatments per day) each week for 2 weeks. Sham Control Treatment group (i.e., identical rTMS experimental procedure, but no active stimulation) will receive the same frequency and duration of rTMS sessions. The proposed rTMS protocol is consistent with the FDA approved treatment regimen employed for major depressive disorders at the VAPAHCS MIRECC. Magnetic resonance imaging (MR) will be completed prior to rTMS treatment and used to localize the left DLPFC in each participant to optimize rTMS for this region. Active and Sham rTMS groups will complete predictive measures [i.e., MR measures of anterior frontal glutamate:glutamine ratio (Glx), blood flow and tissue volume] prior to the inception of rTMS treatment (baseline) and other outcome measures (i.e., measures of craving, mood, anxiety) immediately pre- and post-completion of the 2 weeks of rTMS sessions. Measurement of baseline anterior frontal Glx, blood flow levels, and tissue volumes is necessary to establish potential biomarkers for prediction of rTMS treatment response, which is requisite for therapeutic optimization. For the 6 months following completion of active or sham rTMS treatment, participants will be contacted monthly, via telephone or in person, to complete a brief standardized measure of alcohol and substance use, as well as craving, to assess for changes in these variables over the previous 30 days. This project will deliver completely novel data on the effica...