OBJECTIVE To study if low dose Unfractionated heparin (UFH) is as effective and safe as Low-molecular weight heparin (LMWH) and also economical as a prophylactic agent for venous thromboembolism in medically ill patients. METHODS A prospective double blind randomised controlled trial consisting of 92 patients fulfilling the inclusion criteria who were admitted to Bangalore Baptist Hospital, Bengaluru, between March 2008 and July 2009 were randomised to receive Unfractionated heparin (UFH) or Low-molecular weight heparin (LMWH). RESULTS The result based on intention to treat (ITT)analysis with best outcome scenario: in the UFH arm there were 47 (97.9%) patients who had not developed DVT/PE as compared to 42 (95.5%) in the LMWH arm. The difference in proportion of patients who had not developed DVT/PE between UFH and LMWH was 2.4% (-5.0, 9.8). The results based on per protocol analysis: In the UFH arm there were 44 (97.8%) patients who had not developed DVT/PE as compared to 39 (95.1%) in the LMWH arm. The difference in proportion of patients who had not developed DVT/PE between the UFH and LMWH arm was 2.7% (-5.2, 10.5). Patients on UFH had higher major bleeding complications 4 (8.9%) as compared to 0 in LMWH arm. But with respect to other complications like thrombocytopenia (HIT) and mild or minimal bleeding both arms were comparable. CONCLUSIONS This study has demonstrated that low dose UFH is as effective as LMWH as a prophylactic agent for venous thromboembolism in medically ill patients and economical also.