Background: Significant hemodynamic, hormonal, and metabolic impairment of a brain-dead organ donor is often associated with the deterioration of graft viability. This study aimed to compare the effect of heparin therapy as a therapeutic dose after brain death confirmation on early graft survival in kidney and liver recipients. Method and Materials: The deceased donors were sorted into two groups based on their D-dimer level. After confirming brain death, one group was given a heparin injection (case group), while the other group did not receive any heparin (control group). A total of 71 brain death donors and matched kidney and liver transplants were included in the case group. A total of 43 brain death donors and matched kidney and liver transplants were included in the control group. A total of 5000 units of heparin were administered every 6 hours to the deceased donor case group. Results: The mean age of the case and control groups were 36.27 \pm 16.13 and 36.15 \pm 18.45, respectively. An independent t test showed that there were no differences between the number of procured organs in both groups (p = 0.29). There was no significant difference between the graft survival rate and the doses of heparin injection to the liver recipients (p = 0.06). However, a significant difference was revealed between the graft survival rate and the dose of heparin injection (p = 0.004) in kidney recipients. Conclusions: The data suggest that administering low therapeutic doses of heparin to donors before organ donation may potentially prevent thrombosis and provide a protective benefit. We showed that heparin therapy had no significant effect on the number of donated organs and graft survival.