Prostate cancer (PCa) is one of the most common types.Eearly diagnosis is important for PCa control.However, prostate-specific antigen (PSA)is organ-specific and can lead to unnecessary and/or repeat biopsies because of its unsatisfactory sensitivity and specificity.Using the IlluminaInfinium Human Methylation 450 BeadChip array, we epigenotyped methylated sites in cancer tissues and normal adjacent tissues from 66 patients.We found that compared with normal adjacent tissues there were 6 aberrant methylation sites in cancer tissues on the Y-chromosome.Through pyrosequencing using urine of PCa patients, we finally identified one methylated site (cg05163709) on the Y-chromosome as a potential biomarker.We evaluated the predictive capacity of the aberrant methylated site using the area under receiver operating characteristic (ROC) curve (AUC).The ROC analysis showed a higher AUC for cg05163709 (0.944) than prostate-specific antigen (PSA;0.753).These results indicate that aberrant DNA methylation of cg05163709 on the Y-chromosome is a potential diagnostic marker with high sensitivity (93.9%) and specificity (83.3%).