Aim. To evaluation of thyroid function in neonates born from mothers affected by thyroid disease in order to define follow-up thyroid function test is needed for these children. Methods: Records were reviewed for all newborn with thyroid dysfunction of mothers who were born in Cheill General Hospital, from May, 2012 to May, 2015. All neonates were tested for thyroid function by measurement of thyroxine and TSH in 3rd or 4th day. Neonates who were born from women with thyroid disease and having anti-thyroglobulin or anti-microsomal antibodies were assigned as group I, women with hypothyroidism who did not have autoantibodies were assigned as group II, and women without thyroid problems were assigned as group III. Results In group I, 12(6.1%) infants were diagnosed with compensated hypothyroidism and started levothyroxine therapy. 24(12.2%) infants had transient hyperthyrotropinemia. The median period of normalization of TSH was 112.7 days. Especially, 5 neonates were diagnosed with hypothyroidism, despite of normal results of 1st screening test. 35 infants (9.7%) in group II had hyperthyrotropinemia at 1st test. 9 (2.5%) of them were diagnosed with compensated hypothyroidism and started levothyroxine therapy. The median age of diagnosis of hypothyroidism was 70.4 days. 64 (17.7%) infants had transient hyperthyrotropinemia. The median period of normalization of TSH was 117.5 days. Especially, 3 neonates were diagnosed with hypothyroidism, despite of normal results of 1st screening test. In group III, 468 infants had hyperthyrotropinemia at the 1st test and a spontaneous completely normalization of TSH value was observed. 47 of them were diagnosed with compensated hypothyroidism and started levothyroxine therapy. Conclusion Transient hyperthyroxinemia above the normal reference value for age is frequently observed in the first month of life in infants born from mothers affected by thyroid disease. According to our experience, follow-up is recommended in these newborns; the most accurate and not invasive way to carefully monitor these infants after neonatal screening for TSH seems to be serum-testing TSH between 2nd and 4th week of life. Newborn infants born from women with thyroid disorders should be followed closely for thyroid dysfunction.