In all vertebrates, the neuroendocrine system serves as the primary and essential link between the external and internal environments and a multitude of physiological systems, including the reproductive system. In response to changes in the environment and fluctuations in levels of circulating humoral agents, the neuroendocrine system is able to reverse, maintain or advance physiological events. Endocrine disrupting compounds are believed to wreak havoc on reproduction and development by interfering in the normal flow of information along the brain-pituitary-gonad axis. While the final effects of these compounds may be easily determined in a number of species, utilization of non-traditional research animals, such as some fishes in which the pattern of information flow along the brain-pituitary-gonad axis has been meticulously detailed and documented, will provide excellent and novel means of elucidating not only the final effects but the cytological, histological and systemic mechanisms of action of these endocrine disruptors. This report presents methods of assessing the effects of endocrine disrupting compounds on a variety of physiological and morphological parameters in fishes.