Today, there have been spectacular advances in surgical techniques, organ preservation for transplantation, optimal and efficient donor and recipient selection, more efficient diagnosis of transplant complications, and major progress in pharmacological immunosuppression procedures. In this regard, survival rates after transplantation of various organs have been gaining ground, particularly in the case of lung transplants, whose average survival rate is lower than other types of transplants. In this regard, it is important to detect acute and subclinical clinical rejection, as well as chronic allograft rejection. This is especially important in heart and lung transplants. In the latter type of transplant, and due to the chronic dysfunction of the lung allograft, it is key to detect rejection early and promptly, as it can affect up to half of the transplant patient population. Therefore, effective diagnostic tools are needed to visualize the level of allograft damage using genomic methods such as those that measure donor-derived cell-free DNA (dd-cfDNA). The plasma concentration of dd-cfDNA increases after graft injury or infection. Our team has experience quantifying this parameter in allograft injury progression, and our experience and comparison with the published literature will be presented in the following sections, discussing validated and non-validated results.