The intricate nature of the vertebrate endocrine system creates several challenges that impede the understanding of the threats that endocrine disrupting substances (EDS) may pose to both humans and wildlife. While there are many similarities in the organization of endocrine communication across vertebrate classes, there are differences in hormonal activities and regulated events which makes generalizing EDS effects across species difficult. Aspects of endocrine functioning that may be affected by EDS include the biosynthesis, transport or availability, and metabolism of hormones. Also, EDS may interact with hormone receptors, which is a feature exploited by researchers as a screening method to identify potential EDS. There are many factors to consider in regards to the effects of potential EDS on endocrine functioning, including the timing of exposure, species-specific differences, and a multitude of other factors, which may impinge directly on the physiological endpoints used to determine if endocrine disruption has occurred. It is important to understand the status of the endocrine system before attempting to interpret reproductive status or the general health of the population. This paper provides an overview of the endocrine physiology of vertebrates and a description of the mechanisms by which EDS may affect endocrine function. As well, some of the factors that complicate our understanding of the relationship between exposure to EDS and compromised health in different vertebrate species are included.