Organ transplantation is the treatment of choice for patients with end-stage organ failure. The donor organ in the recipient body experiences several immune and non-immune related insults. Improved immunosuppressive drugs and surgical techniques and procedures have helped in the short-term outcome in terms of graft survival. However, in the absence of effective and specific methods of monitoring the transplanted organ, the long-term outcome is still far from satisfactory. Currently available methods are far from optimal as they are either not specific or are invasive. This reality has inspired several groups to look for more effective and semi- or noninvasive methods of diagnosis of transplant injury. Cell-free deoxyribonucleic acid (cfDNA) has been considered a diagnostic biomarker for different health issues including transplant injury. In this review, we have summarized the current status of the utility of cfDNA measurement in the blood and biofluids of solid organ transplant patients as a non-invasive biomarker of allograft injury.