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Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited cause of chronic kidney disease with <i>Polycystin</i> (<i>PKD</i>) 1 and 2 gene mutation. However, the intra-familial variability in symptoms further suggests a non-Mendelian contribution to the disease. Our goal was to find a marker to track the epigenetic changes common to rapidly progressing forms of the disease. The risk of ADPKD increases with age, and aging shortens the telomere length (TL). Telomeres are a nucleoprotein structure composed mainly of three complexes, shelterin, CST and <i>RNA-containing telomere repeat</i><i>(TERRA)</i>, which protects the ends of chromosomes from degradation and fusion, and plays a role in maintaining cellular stability and in the repair of telomeric damage. <i>TERRAs</i> are transcribed from telomeric regions and a part of them is engaged in a DNA/RNA hybrid (R-loop) at each chromosome end. We tracked TL and <i>TERRA</i> levels in blood samples of 78 patients and 20 healthy control. Our study demonstrates that TL was shortened and <i>TERRA</i> expression levels in the DNA-attached fraction increased in autosomal dominant polycystic kidney patients with mutations in <i>PKD1</i> and <i>PKD2</i> compared to the control group. Moreover, it was observed that the expression of <i>TERRA</i> engaged in the R-loop was higher and the length of telomeres shorter in patients with ADPKD who showed rapid disease progression. Intrafamilial variation in TL and <i>TERRA</i> levels with the same mutation would indicate reliable epigenetic potential biomarkers in disease monitoring.