Endocrine dysfunction is known to occur after traumatic brain injury. The purpose of this study was to examine the incidence of various endocrine dysfunctions after a stroke. The Taiwan National Health Insurance Research Database (NHIRD) was searched from 2001 to 2011 for patients with a diagnosis of stroke. Stroke patients were matched by diagnosis date, age, and sex to patients without a stroke. Cox proportional hazards regression analyses were performed to compare the incidence of goiter, acquired hypothyroidism, thyroiditis, pituitary dysfunction, and disorders of the adrenal glands between stroke and non-stroke patients. There were 131,951 patients in the stroke group, and 131,951 in the matched non- stroke group (mean age 66.1 ± 14.9 years). Stroke patients had significantly higher risk of acquired hypothyroidism (crude hazard ratio [cHR] = 1.65, 95% confidence interval [CI]: 1.44, 1.90; adjusted hazard ratio [aHR] = 1.65, 95% CI: 1.42, 1.91), pituitary dysfunction (cHR = 2.32, 95% CI: 1.79, 2.99; aHR = 1.92, 95% CI: 1.46, 2.52), and disorders of the adrenal glands (cHR = 1.79, 95% CI: 1.52, 2.12; aHR =1.62, 95% CI: 1.36, 1.92) than non-stroke patients. Pituitary dysfunction and disorders of the adrenal glands were found in both hemorrhagic stroke and ischemic stroke patients, while hypothyroidism was seen in ischemic stroke patients only. No significant association was found for goiter and thyroiditis. In conclusions, stroke survivors have an approximately 2-fold increased risk of developing acquired hypothyroidism, pituitary dysfunction, or disorders of the adrenal glands. These risks should be taken into account in the management of patients who have ischemic or hemorrhagic strokes. Graphical Abstract.