Background Preterm infants are at high risk of developing congenital hypothyroidism (CH) due to the immaturity of the hypothalamic-pituitary-thyroid (HPT) axis, loss of iodine supply from the mother and preterm health problems. Objectives To study the incidence and etiologies of CH in preterm infants who were born or admitted in our institute during 2010–2015. Methods The medical records of preterm infants diagnosed with CH as defined by the thyroid-stimulating hormone (TSH) level at the time of the first or second screening >10 mU/L and/or free T4 < 1.00 ng/dL were reviewed. Results Of 2777 preterm infants, 73 cases (2.6%) were diagnosed as CH. The average TSH levels at the first and second screenings were 20.85 and 15.42 mU/L, respectively. The patients were treated with thyroxine at an average initial dosage of 15 μg/kg/day. At 2–3 years of age, after thyroxine discontinuation for 6–10 weeks and regular thyroid function tests for 2 years, 58 patients (79.5%) were diagnosed as having transient CH and 15 patients (20.5%) were diagnosed as having permanent CH. We found no clinical or laboratory parameters in the neonatal period that could differentiate permanent from transient CH. Thyroid scintigraphy (99 m pertechnetate) revealed two patients (13.3%) with ectopic thyroid, one with thyroid hypoplasia (6.7%), eight with normal thyroid (53.3%) and four with enlarged thyroid (26.7%). Conclusions CH was common in preterm infants with an estimated incidence of 2.6%. Thyroxine should be given to preterm infants with higher initial values of TSH >10 mU/L in order to prevent delayed treatment of permanent CH that could be confirmed later.