Value of the Data •The data indicate that cell-free DNA in the plasma after liver transplantation is composed of different groups of cell-free DNA fragments. These groups have different size ranges and Graft-derived cell-free DNA is present mainly in the shorter fragments. •The data will be helpful for understanding the physical characteristics of Gcf-DNA1 in plasma of patients with inborn errors of metabolism after liver transplantation. •The data presented here will be useful for developing a cost-effective and novel non-invasive method to monitor graft injury after liver transplantation