Persons living with HIV (PLWH) are at an increased risk of contraindicated drug-drug interactions (XDDIs), which may result in deleterious outcomes. Study objectives were to (1) compare the frequency of hospitalizations between patients with and without XDDIs and (2) determine if XDDIs are independently associated with hospitalizations in PLWH. A retrospective cohort study was performed among PLWH receiving care at the Upstate New York Veterans' Healthcare Administration or University of New Mexico Truman Health Services from 2000 to 2013. Hospitalization was defined as an admission to an inpatient hospital facility for ≥24 h. Of the 1329 patients evaluated, 149 (11.2%) patients were hospitalized within 1 year of antiretroviral therapy initiation. A significantly higher proportion of patients with XDDIs were hospitalized compared with those who did not have XDDIs (20.3% vs. 10.2%, risk ratio: 1.98, 95% confidence interval [CI]: 1.35-2.91, p = .001). In the multivariate Cox proportional hazards regression analyses, XDDIs were independently associated with hospitalizations (hazard ratio [HR]: 1.58; 95% CI: 1.00-2.48; p = .05), after adjustment for CD4 < 242 cells/mm³ (HR: 2.38; 95% CI: 1.72-3.33; p < .001), protease inhibitor (PI)-based regimen (HR: 1.35; 95% CI: 0.97-1.89; p = .08), recreational drug use (HR: 2.58, 95% CI: 1.85-3.58, p < .001), and non-HIV medications ≥10 (HR: 1.62; 95% CI: 0.97-2.69; p = .07). In this study an increased risk of hospitalization was observed among PLWH with XDDIs compared with those without XDDIs. This relationship persisted after adjustment for CD4 count, use of a PI-based regimen, recreational drug use, and number of non-HIV medications.