Outcomes related to disordered metabolism are common in alcohol dependence (AD). To investigate alterations in the regulation of body mass that occur in the context of AD, we performed a GWAS of BMI in African-Americans (AAs) and European-Americans (EAs) with AD. Subjects were recruited for genetic studies of alcohol or drug dependence, and evaluated using the Semi-Structured Assessment for Drug Dependence and Alcoholism. We investigated a total of 2,587 AAs and 2,959 EAs with DSM-IV AD diagnosis. In the stage-1 sample (N=4,137), we observed three genome-wide significant (GWS) SNP associations, rs200889048 (p=8.98*10−12) and rs12490016 (p=1.44*10−8) in EAs, and rs1630623 (p=5.14*10−9) in AAs and EAs meta-analyzed. In the stage-2 sample (N=1,409), we replicated 278, 253, and 168 of the stage-1 suggestive loci (p<5*10−4) in AAs, EAs, and AAs and EAs meta-analyzed, respectively. A meta-analysis of stage-1 and stage-2 samples (N=5,546) identified two additional GWS signals: rs28562191 in EAs (p=4.46*10−8) and rs56950471 in AAs (p=1.57*10−9). Three of the GWS loci identified (rs200889048, rs12490016, rs1630623) were not previously reported by GWAS of BMI in the general population and two of them raise interesting hypotheses: rs12490016 – a regulatory variant located within LINC00880, where there are other GWAS-identified variants associated with birth size, adiposity in newborns, and bulimia symptoms which also interact with social stress in relation to birth size; rs1630623 – a regulatory variant related to ALDH1A1, a gene involved in alcohol metabolism and adipocyte plasticity. These loci offer molecular insights regarding the regulatory mechanisms of body mass in the context of AD.