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Background: Congenital hypothyroidism (CHT) is one of the most common congenital endocrinal disorders. The prevalence of CHT is estimated about 1 in 3,000 newborns. The prevalence, etiology and associated disorders of abnormal thyroid screening tests are reported in different ranges. In this study, we assessed the pre-term newborns for CHT and associated factors that influence thyroid function. Methods: One hundred newborns with the gestational age fewer than 35 weeks were investigated. Baseline serum thyroid stimulating hormone (TSH) and free thyroxin (FT4) levels were measured during the first 5 days of life and were repeated during the first 5 weeks. We analyzed the effects of demographic factors and the presence of respiratory distress syndrome on the alteration of thyroid function tests during the first 5 weeks of life. Results: The mean gestational age (GA) at delivery was 32.35΁1.97 (range 28 to 35) weeks. CHT was observed in 13(13%) preterm infants. GA was the only factor which affect the FT4 changes over the two weeks follow-up (P < 0.001, b: -2.783, Power: 70.2%) although the differences between baseline and follow-up amount of TSH were not significantly influenced by GA (P = 0.062, power: 46%). However, the adjusted TSH and FT4 serum level changes during follow-up were significantly different between two groups (between CHT and normal, P = 0.006, 0.000, respectively). Conclusions: It seems that thyroid function tests should be repeated in preterm infants, especially for patients with lower gestational age, to confirm the diagnosis of CHT. Also, CHT should be considered among the newborns that are affected by RDS.