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Objective: Hypothyroidism may be an exacerbating factor for primary headaches and migraine is one of the most common primary headaches in childhood. The purpose of this study was to evaluate the effect of treatment of subclinical hypothyroidism on children with migraine headache., Materials & Methods: In a quasi-experimental study, the severity and monthly frequency of headache of 25 migraineur children with subclinical hypothyroidism who were referred to the pediatric neurology clinic of Shahid Sadoughi University of Medical Sciences,Yazd, Iran between January 2010 and February 2011 and were treated with levothyroxine for two months were evaluated., Results: Thirteen girls (52%) and 12 boys (48%) with the mean age of 10.2 ± 2.76 years were evaluated. In children with hypothyroidism, the monthly frequency of headache (mean ± SD: 17.64 ± 9.49 times vs. 1.2 ± 1.1 times) and the severity of headache (mean± SD: 6.24±1.8 scores vs. 1.33 ± 0.87 scores) were significantly decreased by treatment., Conclusion: Based on the results of this study, treatment of subclinical hypothyroidism was effective in reducing migraine headaches. Therefore, it is logical to check thyroid function tests in migraineur children.