The mitochondrial cfDNAs Mito-1 and Mito-2 were higher in metastatic than in non-metastatic patients and controls.Mito-1 and Mito-2 fragment concentration significantly correlated with Fuhrman grade (rs = 0.209 and 0.206, p = 0.0121 and 0.014, respectively)APP-3 fragment concentration decreased in both ccRCC groupsThe cfDNA integrity decreased from controls to metastatic patients. Here, XPNPEP3 is linked to nonpapillary renal cell carcinoma.