Objective: Congenital heart disease (CHD) associated with thyroid disease has been reported in Down syndrome (DS). The purpose of this work was to assess abnormalities of the thyroid in relation to the frequency and type of CHD on admission among children with DS. Methods: This retrospective study included 187 children with DS between August 1993- December 2005. Karyotype analysis, thyroid function tests and echocardiographic studies were performed in patients all children with DS. If necessary, hemodynamic study by catheterization was carried out. Thyrotropin releasing hormone (TRH) stimulation test was performed in having elevated thyroid stimulating hormone (TSH) level. Statistical analyses were performed using Chi-square, “t” test for independent samples or Mann-Whitney U test. Results: It was found that 136 (72.73%) patients with DS had CHD. The age difference at the time of admission was statistically significant for these two groups (p<0.001) in children with /without CHD. There were 12 (11.88%) patients with congenital hypothyroidism and DS, of whom 11 had CHD. There were statistically significant differences in the levels of TSH and total thyroxine (tT4) between congenital and subclinical hypothyroid and euthyroid groups (p<0.001 for TSH and p< 0.001 for tT4). But there was no significant relationship between having any kind of CHD and levels of TSH and tT4. Conclusion: Our data suggest that all patients with DS should be evaluated with careful physical and echocardiographic examination on admission. In addition, congenital or subclinical hypothyroidism should also be kept in mind in children with DS and monitored accordingly.