Thyroid scintigraphy using Tc-99m pertechnetate is a frequently performed procedure in routine nuclear medicine practice. The indications for thyroid scintigraphy are investigation of hyperthyroidism, nodularity of the gland, cause of thyroid stimulating hormone elevation and localization of an ectopic thyroid gland. In the pediatric population, the most common request is for the evaluation of neonatal hypothyroidism. This imaging procedure is helpful in the identification of the underlying cause as well as in making a differential diagnosis. Early diagnosis is essential for appropriate therapy planning in this age group, and thyroid scintigraphy provides important diagnostic data. This article is written to review the scintigraphic findings in various congenital thyroid anomalies and to underline its use in the differential diagnosis.