Background and Objectives: Migraine is caused by genetic susceptibility that is triggered by environmental as well as biological factors, and it is also linked to many somatic comorbidities, including clinical and subclinical hypothyroidism. We aimed to estimate the potential association between subclinical hypothyroidism (ScH) and migraine in children at our tertiary hospital. Materials and Methods: Using a case–control strategy, 200 children and adolescents were assigned to two equal groups: a case group (patients with migraine) of 100 patients and a control group of 100 patients without migraine. Clinical and biochemical parameters (TSH, FT4) were compared between the groups using statistical analysis. Results: Thyroid function comparison between the groups showed higher TSH but normal FT4 among children with migraine headache compared to the control group, which means more frequent ScH cases among the migraine group relative to the control (17% vs. 2%, p < 0.001). Obesity and overweight were more frequent among patients with migraine than the control group (8 and 5% vs. 2 and 1%, respectively). The (overweight/obese) patients with migraine had about 77% ScH and 15.4% overt hypothyroidism compared to 8% ScH and no overt hypothyroidism among normal body weight migraine patients (p < 0.001). No significant difference in the prevalence of nodular goiter between patients with migraine and controls was found. Conclusions: Based on our results, subclinical hypothyroidism is significantly linked to childhood migraine. Obesity and being overweight are more frequent among patients with migraine. Therefore, it may be logical to test the thyroid function in migraineur children, especially those with high BMI. Further studies are recommended to discover the mechanism of this association in children.

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