Acetochlor is a commonly used herbicide in agricultural environments, which can accelerate T(3)-induced metamorphosis in amphibians. However, effects of acetochlor on the thyroid system in fish are still unclear at environmentally relevant concentrations. In this study, expression profiles of thyroid hormone receptor alpha (tralpha), deiodinase (d1 and d2), malic enzyme (me), and sodium iodide symporter (nis) genes were determined in larval and adult rare minnow (Gobiocypris rarus) after exposure to different levels of acetochlor (20, 200, and 2000ng/l) for 21 days, respectively. Furthermore, plasma thyroid hormones (THs) levels in adults were evaluated simultaneously. The results showed that d1, d2, me, and nis mRNA levels were significantly down-regulated in the larvae. Similar expression changes of these genes in female brains were found. However, in adult livers, these gene expressions had no significantly effects, except the tralpha mRNA level significantly up-regulated. These results indicated that exposure to acetochlor could result in tissue-specific alternative expression of TH-related genes in adults. Moreover, the expression of d2 and me showed a positive correlation with plasma T(4) levels in female brains. Therefore, larval development and adult brain of rare minnow could be affected by acetochlor at environmentally relevant concentrations.