Use of herbal medicines among patients receiving Anti-retroviral Therapy (ART) remains by far an uncharacterised phenomenon in Africa and Uganda specifically. We evaluated the use of herbal medicines among patients on ART at the HIV clinic of Mbarara Regional Referral Hospital (MRRH), examined factors associated with their concomitant use and their impact on ART adherence. This was a cross-sectional study among 334 systematically sampled patients receiving ART at the HIV clinic of MRRH from February to April 2010. We collected data on patient demographics, clinical characteristics, perceptions of quality of care received, self-perceived health status, information on ART received, herbal medicines use and ART adherence. Study outcomes were concomitant herbal medicine and ART use, and ART adherence. Descriptive analysis and logistic regression were conducted using Stata10.0. Close to half, 155 (46.4%) reported concomitant herbal medicines and ART use, with 133 (39.8%) using herbal medicines at least once daily. Most (71.6%) used herbal medicines to treat HIV-related symptoms. A majority (92.3%) reported that the doctors were unaware of their use of herbal medicines, 68.5% citing its minimal importance to the attending physician. Most frequently used herbs were Aloe vera (25%) and Vernonia amygdalina (21%). Time since start of ART (OR 1.14 95% CI: 1.01-1.28, for each one year increase), number of ART side effects reported (≥3 vs.≤1, OR 2.20 95% CI 1.13-4.26) and self-perceived health status (Good vs. Poor, OR 0.31 95% CI 0.12-0.79) were independently associated with concomitant herbal medicine and ART use. Concomitant herbal medicine and ART use was not associated with poor ART adherence (OR 0.85 95% CI 0.47-1.53). There is widespread concomitant herbal medicines and ART use among our patients, with no association to poor ART adherence. Patients appear to use these therapies to complement as opposed to substituting ART.