Telomere structure is suggested to be important for chromosome and cell integrity and thereby for cell senescence and immortality. In a search for cDNA encoding proteins that bind specifically to telomere repeat sequences, we used random primer-labeled telomere probes to screen a lambda gt11 Jurkat cDNA library. The clone obtained encodes the central region of the large subunit of replication factor C (RFC), a known activator of DNA polymerase delta. Electrophoretic mobility shift analyses of the binding ability of RFC-glutathione S-transferase (GST) fusion protein to telomere probes revealed that RFC recognizes preferentially 5'-phosphoryl (P) groups but not 3'-hydroxyl (OH) groups at the ends of double-stranded telomere repeats. This structure-specific binding of RFC is supported by the observations that it binds to 3'-OH/5'-P ends in telomere repeats produced by DNase gamma, but not to those produced by 3'-P/5'-OH ends for DNase alpha. These findings suggest a novel function for RFC in telomere stability or turnover.