Exposure to environmental contaminants has been shown to alter normal thyroid function in various wildlife species, including the American alligator (Alligator mississippiensis). Abnormalities in circulating levels of the thyroid hormone thyroxine (T4) have been reported in juvenile alligators from several contaminated lakes in Florida. To further elucidate these functional thyroid abnormalities, this study examines the structure of thyroids and circulating T4 concentrations from juvenile alligators collected from three sites of varying contamination on Lake Okeechobee, Florida. The following variables were used to characterize thyroid morphology: epithelial cell height, width and area, percent colloid, and follicle area. These variables were compared among study sites and between genders. No difference was detected in epithelial cell height, epithelial cell area, or follicle area among the sites, whereas significant differences in epithelial cell width (p = 0.02) and percent colloid (p = 0.008) were found. Animals from the most contaminated site (Belle Glade) had significantly greater epithelial cell widths and significantly less colloid present in their follicles compared to animals from the reference site (West). Gender did not have a significant interaction with site for any variable measured. Thyroxine (T4) concentrations were elevated in the intermediately contaminated site (Conservation Area 3A) compared to the other sites (p < 0.0001). It is proposed that the disruptions seen in Lake Okeechobee alligators are due to disruptions at both the thyroid and extra-thyroidal tissues.