Telomerase, a ribonucleoprotein reverse transcriptase, copies a short portion of its integral RNA moiety (TER) onto telomeres, compensating for losses caused by incomplete replication or degradation. Telomerase attracted widespread interest for its implications in cancer and aging, and as a target for cancer therapy. Non-template portions of TER are important for telomerase function, yet highly divergent in sequence. We have shown that  functional domains are structurally conserved and intimately involved in telomerase function. We predicted a secondary structure model for budding yeast TERs, revealing conserved elements shown by mutational analysis to be important for telomerase function in vivo. Integrating genetic and computational modeling, we predicted three-dimensional structures for two of these functional elements, demonstrating their conservation across yeast, vertebrates and ciliates: a pseudoknot structure with a highly unusual triple helix and a three-way junction binding the telomerase reverse transcriptase protein. We continue studying the structure of TER elements, alternative RNA conformations, protein-RNA interactions, and their involvement in telomerase assembly and function. The functional relevance of our predictions will be studied by yeast genetics and in vitro reconstitution of telomerase activity. Integrating the structural, biochemical and genetic data is promising to advance the understanding of telomerase structure and function, and reveal potential targets for cancer therapy.