Regulation of Thyrotropin Releasing Hormone (TRH) transcription in the hypothalamus represents the central control point of thyroid function. To examine the expression of potential TRH regulatory components, we simultaneously amplified, by semi-quantitative multiplex PCR system, nine key genes from < or = 100 ng total RNA from two brain areas (hypothalamus and cortex) under different thyroid states. Expression of TR1 and TR2 isoforms, key elements in TRH regulation, was modified by thyroid status in the hypothalamus but not in the cortex. Similarly, hypothyroidism increased specifically hypothalamic levels of three co-modulator genes. This study provides the first demonstration of tissue specific co-regulation of a set of genes by thyroid status within a defined brain area.