The genetic basis for differences in thyrotropin (TSH) sensitivity between 2 rat strains was examined using consomic rats generated from original strains SS (TSH 1.8 ± 0.1 ng/ml; Free T₄ Index (FT₄I) 4.9 ± 0.4) and BN (TSH 5.5 ± 0.6 ng/ml p<0.05; FT₄I 4.3 ± 0.1, p not significant). Consomic rats SSBN6 (BN chromosome (CH) 6 placed in SS rat) and SSBN2 (BN CH 2 placed in SS rat) have TSH concentrations intermediate between pure SS and BN strains (2.9±0.3 and 3.1 ± 0.3 ng/ml, respectively; p<0.05). Candidate genes on rat CH 2 included TSH -subunit and on CH 6 the TSH receptor (TSHR). TSH from sera of BN, SS, SSBN6 and SSBN2 strains had similar in vitro bioactivity suggesting that the cause for the variable TSH concentrations was not due to an altered TSH. Physiological response to TSH was measured by changes in serum T₄ concentrations upon administration of bovine TSH (bTSH). Rat strain SS had a greater T₄ response to bTSH than BN (change in T₄, 1.3 ± 0.1 vs. 0.4 ± 0.1 µg/dl, p<0.005), suggesting reduced thyrocyte sensitivity to TSH in BN. Sequencing of the TSHR coding region revealed an amino acid difference in BN (Q46R). This substitution is unlikely to contribute to the strain difference in serum TSH since both TSHR variants were equally expressed at the cell surface of transfected cells and responsive to bTSH. Given similar TSH activity and similar TSHR structure, TSHR mRNA expression in thyroid tissue was quantitated by real time PCR. BN had 54 ± 5% the total TSHR expression compared to SS (100 ±7%, p<0.0001), when corrected for GAPDH expression, a difference confirmed at the protein level. Therefore, the higher TSH level in the BN strain appears to reflect an adjustment of the feedback loop to reduced thyrocyte sensitivity to TSH secondary to reduced TSHR expression. These strains of rat provide a model to study the cis and trans acting factors underlying the difference in TSHR expression.