Background. The human immunodeficiency virus (HIV) epidemic has shifted to more women being infected than in previous years and this has led to more women in care for HIV-related conditions. Substance use continues to play a direct and indirect role in the epidemic among women. Additional research studies on the potential consequences of substance use among women infected with HIV are needed Methods. Using a non-concurrent and concurrent cohort of HIV-infected women, we examine the impact of substance use on a social, behavioral, and clinical consequence---maternal-child separation, potential HIV transmission (sexual risk behavior), and potential HIV infectiousness (genital HIV viral shedding). We focus primarily on alcohol consumption were possible, given its often overlooked role in the substance use and HIV literature. Bivariable and multivariable methods were employed, including methods for analysis of longitudinal data Results. Findings indicate a strong relationship between substance use and selected consequences among women in these samples. Mothers who were current substance users (including alcohol and other illegal drugs) were more likely to be separated from one or more children. Women who were heavier alcohol consumers were more like to participate in sexual risk behaviors, as were women on antiretroviral therapy (ART). Women who were on ART and were heavier consumers were more likely to be shedding HIV in the genital tract Conclusions. Results point to the potential for secondary HIV transmission among these women and to two diverging future research needs---one etiologic in nature and one that incorporates and evaluates screening, intervention and harm reduction measures to ameliorate the social and behavioral consequences associated with substance use in this population. Much remains to be known about how women with HIV manage the mothering role and the role of antiretroviral therapy in these women's lives, especially the potential pharmacokinetic interaction between ART and alcohol consumption. Identification of substance abuse and treatment for it should be a central component of HIV care for women