R-loops are three-stranded nucleic acid structures composed of a DNA–RNA hybrid and a displaced DNA strand. The long noncoding RNA TERRA forms R-loops at telomeres influencing the telomeric chromatin composition and impacting on telomere maintenance mechanisms by semiconservative DNA replication, homology directed DNA repair and telomerase. Here, we describe a method to detect R-loops at telomeres, which involves immunoprecipitation with the R-loop recognizing S9.6 antibody, followed by detection of telomeric DNA by either dot-blot hybridization with a radiolabeled telomeric probe, or qPCR using DNA primers that are specific for subtelomeric sequences.