Findings from a recent study describing prevalence of common disease conditions in the largest documented cohort of individuals with Down syndrome (DS) in the United States strongly suggested significant disparity in endocrine disorders among these individuals when compared with age- and sex-matched individuals without DS. This retrospective, descriptive study is a follow-up report documenting prevalence of 21 endocrine disorder conditions, across 28 years of data, from 6078 individuals with DS and 30,326 age- and sex-matched controls, abstracted from electronic medical records within a large integrated health system. Overall, individuals with DS experienced higher prevalence of adrenal insufficiency and Addison’s disease; thyroid disorders, including hypothyroidism, hyperthyroidism, Hashimoto’s disease, and Graves’ disease; prolactinoma/hyperprolactinemia; diabetes insipidus; type I diabetes mellitus; and gout. Conversely, those with DS had lower prevalence of polycystic ovary syndrome and type II diabetes mellitus. Many prevalences of endocrine conditions seen in individuals with DS significantly differ relative to their non-DS matched counterparts. These varied findings warrant further exploration into how screening for and treatment of endocrine conditions may need to be approached differently for individuals with DS.