The thyroid plays an important role in development and is of primary importance in metabolism and heat loss for cetaceans, including the harbor porpoise (Phocoena phocoena). Several studies have demonstrated that environmental contaminants can alter various aspects of thyroid function in mammals and may contribute to various histologic changes. The present study completes the data set of a 2006 study by Das et al., by performing histological and immunohistologic investigations on thyroids of 36 harbor porpoises from Belgian and United Kingdom waters. The number and mean diameter of follicles (μm) and the relative proportion of follicular, connective, and vascular tissue (%) were quantified in the thyroid gland of each individual. Interfollicular fibrosis has been observed in these thyroid glands, and the collective findings support the hypothesis of an endocrine disruption of thyroid function through organochlorinated compounds. Our study aimed also to reveal potential relationships between thyroid morphometric data and metal levels (Cd, Fe, Zn, Cu, Se, and Hg) using multivariate statistical analysis. The multiple regressions revealed statistically significant relationships between trace elements (cadmium, selenium, and copper) and thyroid fibrosis. The largely negative relationships are interesting findings but do not support the hypothesis that these elements have an adverse effect on thyroid morphometry. Further research is needed to understand the nature of any relationship between organochlorine and trace element exposure and thyroid gland morphology and function in harbor porpoises.