Human telomerase uses a portion of its integral RNA component (hTER) as the template to synthesize telomeres at chromosome ends. hTER sequence polymorphisms have been observed in some patients with bone marrow failure syndromes such as aplastic anemia, but the functional significance of most such variants is unknown. Here, we report the functional characteristics of ten previously-described and two newly discovered hTER disease-associated polymorphisms. Most of these hTER variants adversely affected telomerase enzymatic function as measured in the telomerase reconstituted human cells. Similar loss-of-function effects were also seen directly in primary lymphocytes collected from two of the patients. The majority of the functional deficits stemmed from perturbations of the predicted hTER RNA secondary structure, and corresponded well with the degrees of telomere shortening observed in patients. In contrast, hTER variants anticipated to be inconsequential polymorphisms, which were also found in healthy subjects, did not interfere with telomerase function. Loss of telomerase activity and of telomere maintenance resulting from inherited hTER mutations may predispose some patients to aplastic anemia and other marrow failure disorders.