NGFI-B and RNR-1 are closely related transcription factors that constitute a distinct subclass within the steroid/thyroid hormone receptor superfamily. They have been implicated in neuronal differentiation, neuroendocrine regulation of adrenocortical function and T-cell apoptosis. In this study, we measured and compared NGFI-B and RNR-1 mRNA levels in various adult rat tissues and in the developing rat brain by means of the quantitative reverse transcription-polymerase chain reaction. The use of RNA standards synthesized in vitro allowed direct comparison of the amount of the transcripts of these two genes. We demonstrated that the transcripts of both genes were present in all tissues examined although the expression levels widely varied. We found the highest constitutive expression of both genes in the pituitary. High levels of NGFI-B were also expressed in the cerebral cortex, muscle, ventral prostate, thymus and adrenal glands, whereas high levels of RNR-1 expression were restricted to the pituitary and cerebral cortex. These findings were consistent with the notion that NGFI-B and RNR-1 are involved in various signal transduction systems in diverse cell types. The amount of NGFI-B mRNA was greater than that of RNR-1 mRNA in all adult rat tissues, with the highest ratio of NGFI-B relative to RNR-1 expression in the muscle and leukocytes. In contrast, fetal rat brain showed relatively high RNR-1 gene expression. These findings suggested that the NGFI-B and RNR-1 genes are differentially expressed in a tissue-specific and developmentally regulated manner.