Substance abuse treatment (SAT) is important for HIV medical care. Characteristics of those who choose SAT and effects of SAT on HIV clinical outcomes are not understood. We compared patients who enrolled and did not enroll in a SAT program offered within an HIV clinic, and evaluated the effect of SAT on CD4 T-cell counts and HIV plasma viral load (VL). Subjects were assessed and invited to enroll in SAT. Enrollees chose to receive psychological and psychiatric treatment, or motivational enhancement and relapse prevention, or residential SAT. We used logistic regressions to determine factors associated with enrollment (age, race, sex, HIV transmission risk factors, CD4 T-cell counts, and VL at assessment). A two-period (assessment and six months after SAT) data analysis was used to analyze the effect of SAT on CD4 T-cell count and log VL controlling for changes in HIV therapy. We find that, compared to Decliners (N=76), Enrollees (N=78) were more likely to be females (29.5% vs. 6.6%, OR=5.32, 95% CI 1.61-17.6), and to report injection drug use (IDU) as the HIV transmission risk factor (23.1% vs. 9.2%, OR=3.92, CI 1.38-11.1). Age (37.2 vs. 38.4), CD4 T-cell count (377.3 vs. 409.2), and log VL (3.21 vs. 2.99) at assessment were similar across the two groups (p>0.05). After six months, Enrollees and Decliners' CD4 T-cell counts increased and log VL decreased. SAT did not affect the change in CD4 T-cell count (p=0.51) or log VL (p=0.73). Similar results were found for patients with CD4 T-cell count ≤350 at assessment. In this small sample of HIV-infected patients with a limited follow-up period, women were more likely to enroll in SAT than men, and SAT reached those who needed it, e.g., IDUs. We did not find an effect of SAT on HIV clinical outcomes.