The intrathyroidal cytokine gene expression in human autoimmune thyroid disease is difficult to interpret because surgical specimens mostly reflect the autoimmune disease at a late stage. Because it is not possible to investigate early stages of thyroiditis in humans, the Bio Breeding/Worcester (BB/W) rat was used as a model. To characterize the lymphocytic thyroiditis (LT) of BB/W rats further and to evaluate early increases of cytokine gene expression in LT, we investigated the interleukin (IL)-2, -4, -6, -10, -12p40, interferon-gamma (IFN-gamma) and tumor necrosis factor-alpha (TNF-alpha) gene expression in the thyroids, spleens, and livers of BB/W rats with and without histological evidence for thyroiditis. The gene expression of these cytokines was determined by Genescan (PE Applied Biosystems, Foster City, CA) fragment analysis using reverse polymerase chain reaction (RT-PCR). Serum thyroglobulin (Tg) antibody concentrations were measured and the extent of lymphocytic infiltration of one thyroid lobe was histologically graded. Cytokine gene expression in rats with and without LT was compared in three groups of rats: 55-day-old rats after 24 days of iodine administration, 75-day-old rats after 45 days of iodine administration, and 101-day-old rats. In the thyroids of the BB/W rats no expression of IL-4 or IL-10 was detectable. The number of rats with detectable TNF-alpha, IFN-gamma, IL-2, IL-12p40 gene expression was significantly higher in rats with LT. Rats with LT had significantly higher IL-12p40 mRNA levels. There were no significant differences in the IL-6 gene expression between rats with and without LT. A correlation between the level of lymphocytic infiltration and the TNF-alpha (r = 0.56, p < 0.0065) and TG antibody concentration (r = 0.62, p < 0.0065) was found. Therefore, the early cytokine gene expression in the BB/W rat is characterized by Th1-related cytokines like IL-2 and IFN-gamma. Whether the detected IL-12p40 (10 rats) and IFN-gamma (5 rats) gene expression in animals without LT is an early indicator for the development of LT remains to be determined.