 The intersection of HIV-related health outcomes and problem substance use has been well documented. New York City continues to be a focal point of the U.S. HIV epidemic. In 2011, the NYC Department of Health and Mental Hygiene (NYC DOHMH) issued a recommendation that all HIV infected individuals should be offered antiretroviral therapy (ART) regardless of CD4 cell count or other indicators of disease progression. This policy is based in the concept of “treatment as prevention,” in which providing ART to people living with HIV (PLWH) greatly reduces the likelihood of HIV transmission, while also improving individual health. The “ART for ALL” (AFA) study was designed to inform modifications to and identify gaps in the implementation of universal ART, and specifically to help guide allocation of resources to obtain local policy goals for increasing viral suppression among PLWH who have problem substance use.