Aim: It was the aim of this study to describe the presentation and clinical course of Hashimoto’s thyroiditis (HT) in children with Down’s syndrome (DS) in 2 Scottish health regions. Patients and Methods: We retrospectively analysed clinical, biochemical and thyroid antibody status in 38 patients with DS with HT diagnosed from 1989 to 2004. Results: The sex distribution was similar (20 males, 18 females), with a median age of 12.3 years (range 2.1–17.7). Of the 38 patients reviewed, 29 were identified by screening. A goitre was present in 6/38 patients. Thyroid antibodies were positive in 36/38 patients, negative in 1/38, and data were unavailable for 1/38. At presentation, 37/38 patients were hypothyroid: 21/37 with compensated hypothyroidism (6 treated initially) and 16/37 with decompensated hypothyroidism (all treated). Of the 15/21 compensated patients who were untreated initially, only 3 remitted while 12 showed disease progression prompting treatment. In the decompensated group, 1/16 patient pursued a fluctuating course between hypo- and hyperthyroidism. The final patient, who was hyperthyroid at presentation, also showed marked fluctuation in thyroid function over a 5-year period. Conclusion: The natural history of HT in DS is unusual, with no female predominance and infrequent goitre in our cohort. While almost all patients required treatment eventually, clinicians should be aware that the disease may pursue a fluctuating course between hypo- and hyperthyroidism.