Prompt antiretroviral therapy (ART) initiation after AIDS diagnosis, in the absence of certain opportunistic infections such as tuberculosis and cryptococcal meningitis, delays disease progression and death, but system barriers to inpatient ART initiation at large hospitals in the era of modern ART have been less studied. We reviewed hospitalizations for persons newly diagnosed with AIDS at Grady Memorial Hospital in Atlanta, Georgia in 2011 and 2012. Individual- and system-level variables were collected. Logistic regression models were used to estimate the odds ratios (ORs) for ART initiation prior to discharge. With Georgia Department of Health surveillance data, we estimated time to first clinic visit, ART initiation, and viral suppression. In the study population (n = 81), ART was initiated prior to discharge in 10 (12%) patients. Shorter hospital stay was significantly associated with lack of ART initiation at the time of HIV diagnosis (8 versus 24 days, OR: 1.14, 95% confidence interval: 1.04-1.25). Reducing barriers to ART initiation for newly diagnosed HIV-positive patients with short hospital stays may improve time to viral suppression.