The study objectives were to identify opportunities to improve the quality of care in resource-limited settings by examining the workflow and patient activities at two large outpatient HIV clinics in Uganda. Using time motion study techniques, we collected detailed data on all activities of patients and clinicians in two government-sponsored HIV clinics in Uganda. Processes measured included amount of time clinicians (physicians, nurse practitioners and clinical officers) spend in clinic, the daily patient census and patient visit-length. We also recorded the time spent on various activities by providers and patients. We found that the mean time in clinic per workday at Masaka was 5.5 hours and at Mbarara 4.9 hours, with about 60% of this time spent in direct and indirect care of patients at both sites. Workday start-times varied by two hours in Masaka and one-and-a half hours in Mbarara and end-times by five and three hours respectively. One-hundred-and-nineteen patients (SD 34) visited Masaka each day and 107 (SD 45) visited Mbarara. The mean duration of the patient visit was 77 minutes at Masaka and 196 minutes at Mbarara, with 66% and 62% of the time spent at respective sites waiting for care. We conclude that clinicians in resource-poor settings spend limited amounts of time at the clinic site, with a large portion of the clinic-time taken up by tasks that do not require specialized patient-care skills. This study demonstrates that opportunities exist to improve clinic productivity and visit experience for patients, and provides a baseline for designing and evaluating the impact of process improvement interventions.