BACKGROUND: Deep venous thrombosis (DVT) and its major complication pulmonary embolism (PE) are collectively known as venous thromboembolism. In Uganda, the prevalence of DVT among HIV patients has not been previously published. The aim of the study was to determine the prevalence and sonographic features of lower limb deep venous thrombosis among HIV positive patients on anti-retroviral treatment (ART). METHODS: This was a cross sectional study in which HIV positive patients on ART were recruited from an out-patient HIV clinic at Mulago National Referral Hospital. Patients were randomly selected and enrolled until a sample size of 384 was reached. Study participants underwent compression and Doppler ultrasound studies of both lower limb deep veins using Medison Sonoacer7 ultrasound machine. RESUTS: We found a prevalence of DVT of 9.1% (35 of 384 participants) among HIV patients on ART. The prevalence of latent (asymptomatic) DVT was 2.3%. Among 35 patients with DVT, 42.8% had chronic DVT; 31.1% had acute DVT and the rest had latent DVT. Among the risk factors, the odds of occurrence of DVT among patients with prolonged immobility were 4.81 times as high as in those with no prolonged immobility (p = 0.023; OR = 4.81; 95% CI 1.25-18.62). Treatment with second line anti-retroviral therapy (ART) including protease inhibitors (PIs) was associated with higher odds of DVT occurrence compared with first line ART (p = 0.020; OR = 2.38; 95% CI 1.14-4.97). The odds of DVT occurrence in patients with a lower CD4 count (< 200 cells/µl) were 5.36 times as high as in patients with CD4 counts above 500 cells/µl (p = 0.008). About 48.6% patients with DVT had a low risk according to Well's score. CONCLUSION: DVT was shown in nearly 10% of HIV patients attending an out-patient clinic in an urban setting in Uganda. Risk factors included protease inhibitors in their ART regimen, prolonged immobility, and low CD4 count (< 200 cells/µl). Clinicians should have a low threshold for performing lower limb Doppler ultrasound scan examination on infected HIV patients on ART who are symptomatic for DVT. Therefore, clinicians should consider anti-coagulant prophylaxis and lower deep venous ultrasound screening of patients who are on second line ART regimen with low CD4 cell counts and/or with prolonged immobility or hormonal contraception.