BackgroundReference intervals are affected by different factors such as lifestyle, ethnicity, age/developmental stage, gender, nutrition and other environmental factors (Clin Biochem Rev: 29,2008). Therefore, it is obvious that it should be established for every population in different regions even within a country. Then the aim of this study is to establish population specific reference intervals of thyroid stimulating hormone, free thyroxine and free triidothyronine levels of cord blood.ResultsOne hundred twenty three cord blood samples collected from the umbilical cord of newborns were analyzed for thyroid stimulating hormone, free thyroxine and free triidothyronine values. The birth weights ranged between 2500 and 4700 g with mean (SD) value of 3241.46 (459.495) gram. Their gestational age ranged between 37 and 44 weeks with an average of 39.74 weeks. The 2.5th and 97.5th percentiles of values were found to be 3.48 mIU/L and 27.57 mIU/L for thyroid stimulating hormone, 0.89 ng/dl and 1.53 ng/dl for free thyroxine and 1.19 pg/ml and 2.51 pg/ml for free triidothyronine respectively.ConclusionIn the present study the reference intervals of thyroid stimulating hormone, free thyroxine and free triidothyronine were established and based on the results obtained, were 3.48–27.56 mIU/L for thyroid stimulating hormone, 0.89–1.53 ng/dl for free thyroxine and 1.19–2.51 pg/ml for free triidothyronine. It has been concluded that the result can provide us with an important baseline to establish population specific reference intervals for our country using large scale studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12887-016-0654-2) contains supplementary material, which is available to authorized users.