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Thyroid dysfunctions are the most common endocrine abnormalities observed in trisomy 21 (T21). The prevalence of thyroid disorders in children with T21 varies between 4% and 40%. Dysregulation of thyroid function, which is specific to T21, is a possible etiology. Thyroid dysfunction can have a significant impact on cognitive development and growth. Transiently abnormal thyroid function tests (TFTs) are frequently observed in T21 and may cause diagnostic confusion. There is a lack of literature on several specific thyroid conditions (such as CH, transient abnormal TFT and thyroid dysfunction) in children with T21 in resource-limited settings. Records of children followed up at the Child Development Clinic dedicated to children with T21 at the university unit of Lady Ridgeway Hospital (LRH), Sri Lanka, were reviewed retrospectively. The prevalence and characteristics of different thyroid dysfunctions were studied. Among the 88 children with T21 (Male: Female ratio of 1.5:1), 35 (39.7%) had thyroid dysfunction. Seventeen (20%) children were managed as congenital hypothyroidism (CH), nine (10.2%) had transiently abnormal TFTs. Acquired hypothyroidism was noted in 8 (9%) children, and two children (2.3%) had hyperthyroidism. Among the 17 children who were managed as CH, 12 (70.5%) were diagnosed during the neonatal period following newborn screening (NBS). The mean TSH level at diagnosis was 22.3 mIU/l (10.6–58). All 17 children had normal ultrasound scans of the thyroid. The average current thyroxine dose in the < 3-year-old group (n = 4) was 2.1 µg/kg/day, and in the ≥ 3-year-old group, it was 2.5 µg/kg/day. The interquartile range(IQR) for age at diagnosis of acquired hypothyroidism was between 7years 9months to 12years 8 months. In those managed as transiently abnormal TFTs, the time taken for TFTs to normalise (without any treatment) ranged widely between six weeks and eight months. Thyroid dysfunction is a commonly encountered challenge in managing T21. Transiently abnormal TFTs are common and require close observation. Gland-in situ CH (GIS-CH) is increasingly being detected among this population. The cost-effectiveness of using genetic analysis in GIS-CH in resource-limited settings needs to be studied. Differentiating transient CH from permanent CH is quite challenging in clinical practice, although the low thyroxine dose requirement, especially after 3 years of age, may provide valuable information. Further longitudinal studies are needed to delineate the prevalence of transient vs. permanent CH.