Mitochondrial injury contributes to renal dysfunction in several models of renal disease, but its involvement in human hypertension remains unknown. Fragments of the mitochondrial genome released from dying cells are considered surrogate markers of mitochondrial injury. We hypothesized that hypertension would be associated with increased urine mitochondrial DNA (mtDNA) copy numbers. We prospectively measured systemic and urinary copy number of the mtDNA genes COX3 and ND1 by quantitative-PCR in essential (EH, n=25) and renovascular (RVH, n=34) hypertensive patients, and compared them with healthy volunteers (HV, n=22). Urinary kidney injury molecule (KIM)-1 and neutrophil gelatinase-associated lipocalin (NGAL) served as indices of renal injury. Renal blood flow (RBF) and oxygenation were assessed by multidetector-CT and BOLD-MRI. Blood pressure, urinary NGAL and KIM-1 were similarly elevated in EH and RVH, and estimated glomerular filtration rate (eGFR) lower in RVH versus HV and EH. RBF was lower in RVH compared to EH. Urinary mtDNA copy number was higher in hypertension compared to HV, directly correlated with urinary NGAL and KIM-1, and inversely with eGFR. In RVH, urinary mtDNA copy number correlated directly with intra-renal hypoxia. Furthermore, in an additional validation cohort, urinary mtDNA copy number was higher in RVH compared to HV subjects (n=10 each). The change in serum creatinine levels and eGFR 3-months after medical therapy without or with revascularization correlated with the change in urinary mtDNA. Therefore, elevated urinary mtDNA copy numbers in hypertensive patients correlated with markers of renal injury and dysfunction, implicating mitochondrial injury in kidney damage in human hypertension.