Effects of perchlorate on sodium-iodide symporter (NIS) and pendrin gene expression in deer mice kidney and stomach were investigated. This was accomplished by isolating a partial cDNA sequence of deer mice NIS gene of 425 bps, and quantitatively analyzing NIS mRNA expression in various deer mouse tissues. The highest NIS expression level was in the stomach, followed by testes, brain, and large intestine; very low expression of NIS was observed in the lung, kidney, heart, and liver. Exposure to perchlorate through drinking water for 28 days did not significantly increase NIS gene expression in the kidney and stomach, and pendrin gene expression in the kidney. In a depuration experiment in which deer mice were exposed to perchlorate for 8-h followed by an 88-h depuration period, no significant difference was observed between the low and high exposure groups in terms of NIS or pendrin gene expression in the kidney or stomach at the end of the experiment. Furthermore, no significant linear relationship was observed between gene expression (either NIS or pendrin) in the kidney and perchlorate mass excreted via urine at day 28, average daily excretion, or total excretion mass over the 28 day exposure. Several factors could influence the effect of perchlorate exposure on NIS and pendrin gene expression in the stomach and kidney, including (1) pre-exposure to trace perchlorate through food and water perhaps resulting in adaptation (or tolerance) in these animals; (2) metabolism of perchlorate in deer mice causing only 46-61% perchlorate excreted into urine. It is also possible that there is no effect of perchlorate exposure and/or urinary excretion on NIS and pendrin gene expression, particularly in the kidney.