Human herpesvirus-6 (HHV-6) is a ubiquitous betaherpesvirus with immunomodulating properties that have been suggested to play an important role in the development of several autoimmune disorders. Although the primary targets for HHV-6 replication, both in vitro and in vivo, are CD4+ and CD8+ T lymphocytes, some studies have reported the presence of HHV-6 sequences in different solid organs, including in the thyroid gland, showing possible involvement of this herpesvirus in development of autoimmune thyroid disease. The aim of this study was to determine loads of HHV-6 in thyroid gland tissue in comparison to those in peripheral blood of patients with autoimmune thyroiditis. Seven patients [women mean age 45 (28-65)] with histologically confirmed autoimmune thyroiditis were enrolled in this study. Fluorescence-activated cell sorting was used to distinguish and sort lymphocyte populations from peripheral blood mononuclear cells of patients. HHV-6 load was determined by real-time PCR for peripheral blood and thyroid gland tissue samples. Additionally, all results from molecular analyses were compared with histological results obtained by light microscopy. Viral load was detected only in one (46 viral copies/ 1×106cells) blood sample; others were under the detection limit of the used kit. However, in all HHV-6 positive tissue samples viral load was detected in the range of 132-1620 viral copies/106 cells. Substantial HHV-6 load in lymphocyte subpopulations was detected in two of seven patients. HHV-6 load was detected in NK and CD95+ cells of two patients. The obtained results show that thyroid gland cells (tyrocytes) act as target cells for HHV-6.