We have examined the tissue-specific mRNA expression of ERa and ERP in various bovine tissues using real-time RT-PCR. The goal of this study was to evaluate the deviating tissue sensitivities and the influence of the estrogenic active preparation RALGRO on the tissue-specific expression and regulation of both ER subtypes. RALCRO contains Zeranol (alpha -Zearalanol), a derivative of the mycotoxin Zearalenon, shows strong estrogenic and anabolic effects, and exhibits all symptoms of hyperestrogenism, in particular reproductive and developmental disorders. Eight heifers were treated over 8 weeks with multiple-dose implantations (0x, 1x, 3x, 10x) of Zeranol. Plasma Zeranol concentration, measured by enzyme immunoassay, of multiple treated heifers was elevated. To quantify ERa and ERP transcripts also in low-abundant tissues, sensitive and reliable real-time RT-PCR quantification methods were developed and validated on the LightCycler. Expression results indicate the existence of both ER subtypes in all 15 investigated tissues. All tissues exhibited a specific ERa and ERP expression pattern and regulation. With increasing Zeranol concentrations, a significant downregulation of ERa mRNA expression could be observed in jejunum (p <0.001) and kidney medulla (p <0.05). These data support the hypothesis that ERP may have different biological functions than ERa, especially in kidney and jejunum.