Objectives We evaluated the spectrum of diseases accompanying congenital hypothyroidism (CH) in the United Arab Emirates and compared them with internationally studied patterns. Methods The presented retrospective cross-sectional study took place in two government tertiary care centres. In total, 204 patients with a confirmed diagnosis of CH and a minimum period of follow-up of 1 year were included. Patients with Down syndrome, infants born at <35 weeks of gestation, and babies with TORCH (Toxoplasma gondii, Other viruses [HIV, measles, etc.], Rubella, Cytomegalovirus, and Herpes simplex) infections were subsequently excluded from the study. Results Of the subjects with CH, 39% had associated extrathyroidal anomalies (ETAs); among these, 25% had a single anomaly. A significant proportion of Arab males were affected by CH as compared to other ethnic groups. Dyshormonogenesis was the commonest aetiological cause (55%) of CH. Males with an ectopic lingual thyroid gland had significant ETAs as compared to females of the same cohort. The most common ETAs were congenital heart disease (16%), followed by urogenital tract anomalies (14%). Conclusions Detection of a high rate and variability of ETAs associated with CH necessitates the formulation of a structured screening programme including appropriate clinical, laboratory, and imaging tools to detect ETAs at an earlier stage.