Background: Drug-drug interactions (DDIs) are an important cause of adverse drug reactions. The pharmacoepidemiology of such interactions in hospitals in Uganda is not known. Objectives: To determine the prevalence, clinical importance and factors associated with potential DDIs at Mbarara Regional Referral Hospital (MRRH), western Uganda. Methods: Retrospective analysis of 235 randomly selected hospitalization episodes (medication charts and medical notes) from MRRH over a 1-year period from January to December 2008. We collected data on demographics, medications, principal diagnosis, co-morbid conditions and the length of hospital stay. Epocrates Rx was used to identify and classify potential DDIs according to mechanism and management strategy. Descriptive statistics were generated and logistic regression used to determine associated factors. Results: Overall prevalence of potential DDIs was approximately 23% (54 medication charts with at least one potential DDI out of 235 hospitalization episodes). Majority were postulated to occur through a pharmacodynamic mechanism (10.6%) and most required either “use with caution” (11.9%) or “modify treatment/monitor” (10.6%) as a suggested management strategy. After adjusting for confounders: age, sex, hospital department and number of co-morbid conditions, a principal diagnosis of a cardiovascular disease (OR 6.52 95% CI 1.32-32.14) and having 4 or more medicines on the chart (OR 4.30 95% CI 1.98-9.34) were associated with the presence of a potential DDI. Conclusion: Potential DDIs frequently occur at MRRH although most are not clinically significant. Patients with cardiovascular diseases and those who are prescribed multiple medications need to be monitored more closely.