Objective: To explore the feasibility of quantification of testicular DNA methylation from cell-free seminal DNA (cfsDNA), and analyze promoter methylation alterations in men with idiopathic nonobstructive azoospermia (NOA). Design: Comparison between testicular DNA and paired cfsDNA, and among NOA patients with different testicular phenotypes. Setting: Academic research institute and andrology practice. Patient(s): Eighty-eight idiopathic NOA patients with different testicular phenotypes and 24 normozoospermic men. Intervention(s): Testicular biopsies and semen analysis. Main Outcome Measure(s): Five testis-specific methylated promoters were selected. Promoter methylation was quantified using MethyLight in testicular DNA and paired cfsDNA, and the mRNA level was determined by real-time quantitative polymerase chain reaction. Result(s): Correlations of methylation of the selected five promoters between testicular DNA and paired cfsDNA were observed; and promoter methylation was negatively related to the messenger RNA level in testis. The cfsDNA methylation of these promoters showed different dynamic changes among the subtypes of NOA and normozoospermia. Among them, CCNA1 and DMRT1 promoter methylation in the hypospermatogenesis group was higher than in other groups and showed diagnostic potential for the patient with hypospermatogenesis. Conclusion(s): Cell-free seminal DNA could be a novel, noninvasive biomarker for the detection of testicular epigenetic aberrations. Epigenetic information in cfsDNA related to spermatogenesis may serve to predict successful testicular sperm retrieval in NOA patients. (C) 2016 by American Society for Reproductive Medicine.