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Summary SLX4, a scaffold for structure-specific DNA repair nucleases, is important for several types of DNA repair. Many repair proteins bind to sites of DNA damage, resulting in subnuclear “foci,” but SLX4 forms foci in human cells even without DNA damage. Using several approaches, we show that most, but not all, SLX4 foci localize to telomeres in a range of human cell lines irrespective of the mechanisms used to maintain telomere length. The SLX1 Holliday-junction-processing enzyme is recruited to telomeres by SLX4, and SLX4, in turn, is recruited by a motif that binds to the shelterin subunit TRF2 directly. We also show that TRF2-dependent recruitment of SLX4 prevents telomere damage. Furthermore, SLX4 prevents telomere lengthening and fragility in a manner that appears to be independent of telomere association. These findings reveal that SLX4 plays multiple roles in regulating telomere homeostasis., Graphical Abstract, Highlights • The SLX4 DNA repair complex binds to telomeres in different human cell lines • The SLX4 scaffold protein has a TRF2-binding motif responsible for telomere localization • SLX4 also has localization-independent roles at telomeres, SLX4 is a scaffold protein that regulates several DNA repair endonucleases and forms subnuclear foci in human cells that Rouse and colleagues identify as telomeres. SLX4 is recruited to telomeres by a motif that interacts with the shelterin subunit TRF2. Mutations in this motif prevent SLX4 from localizing at telomeres and cause telomeric DNA damage in human cells. SLX4 also has localization-independent roles at telomeres, such as preventing telomere overlengthening.