Introduction:  Chronic kidney disease is high prevalent in the world and associated high morbidity rate. Mitochondria is an organelle for cellular metabolism of bioenergy and higher mitochondrial oxygen radicals’ production that play important role in the renal diseases progression. We hypothesis that urine and plasma cell-free DNA could predict renal damage and prognosis.

Methods: Urine and plasma cfDNA (cell- free deoxyribonucleic acid) were isolated from 140 patients with chronic kidney disease in our study.

Results: The plasma level of neutrophil gelatinase-associated lipocalin (NGAL) is upper as more advanced stage CKD. The plasma cell-free mitochondrial DNA (mitoGE)and nuclear DNA(betaGE) both get lower as the renal function deterioration, in contrast to the mitochondrial copy number(MCN) with insignificant change. There are insignificant changes for urinary cell-free mitochondrial DNA (mitoGE)and nuclear DNA(betaGE) in varying stage of CKD.

There are higher levels of plasma mitoGE and betaGE in good outcome group with insignificant change. The urinary mitoGE is higher in poor outcome group and betaGE is lower in the group with poor outcome.

Conclusions: Mito-GE and beta-GE maybe renal outcome biomarker and predicted the prognosis of chronic renal diseases and early impaired renal function.