BACKGROUND: The close relationship between thyroid disorder and Down syndrome (DS) had been widely reported in the literature. The aim of this study was to assess the prevalence rate and the pattern of thyroid dysfunction in DS in Taiwan. METHODS: A total of 50 Down syndrome (DS) patients from Yang-Ming Home for Disabled, were recruited. In all patients, serum T3, T4, free T4, TSH, thyroid peroxidase antibody (anti-TPO) and anti-TSH receptor antibody were measured. The control group consisted of 212 healthy adults who underwent routine health examination in this hospital. RESULTS: Among 50 DS patients, 8 had subclinical hypothyroidism and one had hyperthyroidism. There was no statistically significant in gender and age between DS and control groups, however, TSH anomaly was significantly higher in the DS group (p = 0.008). Regarding thyroid autoantibodies, anti-TPO was positive in 13 cases (26%) and anti-TSH receptor was positive in 2 cases (4%). Statistically, there was no significant difference in TSH anomaly (p = 0.7), positive anti-TPO antibody (p = 0.097) and positive anti-TSH receptor antibody (p = 1.0) between males and females. The increased TSH levels had no statistically positive correlation with anti-TPO (p = 0.386) or anti-TSH receptor antibody (p=1) in this study. The prevalence of thyroid dysfunction was 18% (9/50) in DS patients in Taiwan. Most of them showed subclinical compensated hypothyroidism (16%, 8/50), and one (2%, 1/50) showed hyperthyroidism. CONCLUSIONS: Thyroid dysfunction is common in DS patients, so periodic thyroid function tests should be performed and early treatment should be given to prevent further intellectual deterioration and improve overall development.