Peptide transporters (Pept) have essential physiological functions and also transport various drugs. Information regarding tissue distribution and gene regulation of Pept in rodents is limited. The present study investigated the distribution of Pept1 and Pept2 mRNA in 19 tissues of male and female Sprague-Dawley rats and C57BL/6 mice, as well as thyroid hormone regulation of renal Pept expression in male rats, using the branched DNA signal amplification assay. Pept1 mRNA was not only highly expressed in small intestine, but also detectable in gonads of both species, kidney of rats, and large intestine of mice. Pept2 mRNA was the highest in kidney, followed by brain and lung. The present study offers the first evidence of considerable Pept2 mRNA expression in pituitary and reproductive organs (testis, prostate, ovary, and uterus). Interestingly, Pept2 mRNA expression in mouse prostate appeared to be much higher than that in rat prostate. Thyroidectomy increased Pept1 and Pept2 mRNA in male rat kidney; such increases were abolished by thyroid hormone replacement.