Background: African American/Black and Hispanic persons living with HIV (AABH-PLWH) in the U.S. evidence insufficient engagement in HIV care and low uptake of HIV antiretroviral therapy, leading to suboptimal clinical outcomes. The present qualitative study used critical race theory, and incorporated intersectionality theory, to understand AABH-PLWH's perspectives on the mechanisms by which structural racism; that is, the macro-level systems that reinforce inequities among racial/ethnic groups, influence health decisions and behaviors. Methods: Participants were adult AABH-PLWH in New York City who were not taking antiretroviral therapy nor well engaged in HIV care (N = 37). Participants were purposively sampled for maximum variation from a larger study, and engaged in semi-structured in-depth interviews that were audio-recorded and professionally transcribed verbatim. Data were analyzed using a systematic content analysis approach. Results: We found AABH-PLWH experienced HIV care and medication decisions through a historical and cultural lens incorporating knowledge of past and present structural racism. This contextual knowledge included awareness of past maltreatment of people of color in medical research. Further, these understandings were linked to the history of HIV antiretroviral therapy itself, including awareness of the first HIV antiretroviral regimen; namely, AZT (zidovudine) mono-therapy, which was initially prescribed in unacceptably high doses, causing serious side effects, but with only modest efficacy. In this historical/cultural context, aspects of structural racism negatively influenced health care decisions and behavior in four main ways: 1) via the extent to which healthcare settings were experienced as overly institutionalized and, therefore, dehumanizing; 2) distrust of medical institutions and healthcare providers, which led AABH-PLWH to feel pressured to take HIV antiretroviral therapy when it was offered; 3) perceptions that patients are excluded from the health decision-making process; and 4) an over-emphasis on antiretroviral therapy compared to other non-HIV related priorities. We found that although participants were located at the intersection of multiple social categories (e.g., gender, social class, AABH race/ethnicity), race/ethnicity and social class were described as primary factors. Conclusions: Critical race theory proved useful in uncovering how macro-level structural racism affects individual-level health decisions and behaviors. HIV clinical settings can counter-balance the effects of structural racism by building "structural competency," and interventions fostering core self-determination needs including autonomy may prove culturally appropriate and beneficial for AABH-PLWH.