Most research done on hypothyroidism has focused on physiological and biochemical aspects of the tissues, whilst there has been little work on tissue morphology especially on salivary glands. The present study has used hypothyroid Wistar rats as a model for investigating the effects of hypothyroidism on submandibular gland structure. Two groups of Wistar rats were studied. One was made hypothyroid with methimazole and the second was an untreated euthyroid group (control). They were euthanised after 10 weeks. Submandibular glands were removed and studied. Systematic random transverse sections were obtained from submandibular glands and subjected to morphometric analysis. Volume density and absolute volume of granular, striated and excretory ducts and interlobular connective tissue were estimated by point counting. Volume-weighted mean particle volume of serous and mucous acini was also determined by unbiased stereology. Absolute volume of granular ducts in the submandibular gland of hypothyroid rats was reduced by approximately 50% (p<0.009) whilst that of the striated and excretory ducts and interlobular connective tissue was unaffected. Volume of serous acini was also significantly (p<0.03) lower in hypothyroid rats. These changes suggest that hypothyroidism has an effect on submandibular gland structure, and that this effect occurs mostly in two major exocrine compartments (granular duct and serous acinus) of the gland.