Alkylphenols such as nonylphenol (NP) are one of a wide variety of environmental chemicals reported to have estrogenic effects in both in vitro and in vivo studies. Induction of hepatic vitellogenin (Vg) gene expression is widely used as a biomarker for xenoestrogen exposure in fish. However, little work has been done to characterize the molecular effects of xenoestrogens on other potential target organs such as the brain. To evaluate brain and liver effects of 4-n-nonylphenol (4-NP), juvenile rainbow trout (Oncorhynchus mykiss) were exposed to waterborne 4-NP or 17β-estradiol (E2). Changes in mRNA levels of salmon gonadotropin-releasing hormone (sGnRH) and estrogen receptor α (ERα) isoforms in the brain and ERα isoforms and Vg in the liver were measured after 3 and 6 days of exposure, with the help of a relative RT-PCR–based quantification method. Fish were treated with increasing doses of 4-NP ranging from 0.01 to 10μM (2.2 μg/l to 2.2 mg/l), and results were compared to the effect of E2 or tamoxifen, a specific ER modulator. In liver, E2 and the highest doses of 4-NP increased Vg and ERα long-isoform mRNA levels within 3 or 6 days of exposure, but 4-NP did not have any effect on ERα short-isoform transcription level. In the brain, 4-NP reduced sGnRH2 gene expression in a dose-dependent manner, but did not modify sGnRH1 or ERα mRNA levels.