Hashimoto's thyroiditis (HT) is the most common of all thyroid diseases and is characterized by abundant lymphocyte infiltrate and thyroid impairment, caused by various cell- and antibody-mediated immune processes. Viral infections have been suggested as possible environmental triggers, but conclusive data are not available. We analyzed the presence and transcriptional state of human herpesvirus 6 (HHV-6) in thyroid fine needle aspirates (FNA) and peripheral blood mononuclear cells (PBMCs) from 34 HT patients and 28 controls, showing that HHV-6 DNA prevalence (82% vs. 10%, p≤0.001) and viral load were significantly increased in FNA from HT patients, and thyrocytes from HT FNA displayed a 100-fold higher HHV-6 DNA load compared to infiltrating lymphocytes. In addition, while HHV-6 was strictly latent in positive samples from controls, a low grade acute infection was detected in HT samples. HHV-6 variant characterization was carried out in 10 HT FNA samples, determining that all specimens harbored HHV-6 Variant A. The tropism of HHV-6 for thyroid cells was verified by infection of Nthy-ori3-1, a thyroid follicular epithelial cell line, showing that thyrocytes are permissive to HHV-6 replication, which induces de novo expression of HLA class II antigens. Furthermore, HHV-6-infected Nthy-ori3-1 cells become targets for NK-mediated killing, NK cells from HT patients show a significantly more efficient killing of HHV-6 infected thyroid cells than healthy controls, and HT patients have increased T-cell responses to HHV-6 U94 protein, associated to viral latency. These observations suggest a potential role for HHV-6 (possibly variant A) in the development or triggering of HT. Hashimoto's thyroiditis (HT) is a very common autoimmune disease of the thyroid. In addition to genetic background, several viruses, including herpesviruses, have been suggested to play a role as possible environmental triggers of disease, but conclusive data are still lacking. The anecdotal presence of human herpesvirus 6 (HHV-6) in HT specimens prompted us to study a possible association between HHV-6 and HT. Our analysis of fine needle thyroid aspirates and blood from HT patients and controls shows that HHV-6 prevalence and load are highly increased in HT patients. Furthermore, HT-derived thyrocytes harbor active virus, whereas HHV-6 is strictly latent in the few virus-positive controls. We also report that HHV-6 infects thyroid cells, inducing de novo expression of HLA-II surface antigens. Consequently, thyrocytes might behave as antigen presenting cells. Interestingly, immune cells from HT patients kill HHV-6-infected thyrocytes more efficiently than controls. Also, HT patients, but not controls, have specific T-cell responses to HHV-6 U94 protein. It is difficult to prove etiologic links between viral infections and diseases, especially in the case of a ubiquitous agent such as HHV -6. Nevertheless, our findings indicate that HHV-6 might contribute to HT development, and argue for a pathogenic association between HHV-6 and HT.