Exposure to a range of environmental endocrine disrupting chemicals is associated with birth defects in several species. High levels of oestrogen, or compounds acting as oestrogen mimics (such as alkyl phenols and pesticides) can alter gene expression and cause sex reversal in fish. In the current study, we use the versatile Zebrafish (Danio rerio) to examine the effect of embryonic exposure to 17β-estradiol (E2) on the development of brain asymmetry and neuroendocrine gene expression. Brain asymmetry was monitored using an assay of parapineal migration, that employs transgenic zebrafish (Tg(foxd3:GFP)) in which the pineal complex is labeled with GFP. The effect of E2 on the hypothalamus and pituitary was assayed using wholemount in situ hybridization (ISH) of previously validated pomc and prl mRNA probes. Embryos were exposed to E2 in aquaria water (0, 100 nM, 1 μM, 10 μM) from for 3 days at 28 °C. At 72 hpf, the embryos were viewed under an microscope equipped to visualise GFP and scored according to the appearance of the parapineal organ (left-handed, right-handed or no migration). Embryos were fixed in 4% paraformaldehyde prior to ISH. Initial results of the parapineal migration assay suggest a decreased incidence of rightward migration of the parapineal organ in embryos exposed to E2 for 72 hpf. There was also an increased incidence of parapineal organ migration failure, suggesting inappropriate exposure to E2 during development could cause migrational defects associated with neurological disorders (e.g. autism, schizophrenia). Neuroendocrine gene expression studies revealed enhanced prl expression in the pituitary of E2-treated embryos, although it was unclear as to whether this represented increased gene expression or lactotroph hyperplasia. Furthermore, the spatial profile of hypothalamic and pituitary pomc expression was also altered by E2 exposure. Collectively, these data suggest that neurological and neuroendocrine changes occur following a short exposure to E2, which may result in abnormal development.