Background: Congenital hypothyroidism, defined as thyroid hormone deficiency at birth, is one of the most common preventable causes of mental retardation. Methods: This study was a cross sectional investigation conducted prospectively on 45,799 live births from September 2010 to February 2012 in the Hormozgan province, Iran, who participated in congenital hypothyroidism screening. In accordance with national protocol, blood samples were taken from the heels of the newborns 3-7 days after their birth. Neonatal TSH values less than 5 mIU / L were considered as normal; TSH values greater than or equal to 5 mIU/L were considered as suspicious, and an immediate report was made to the Focal Point of the newborn's birth place. Descriptive statistics including mean, frequency and percentage were used to present the results. SPSS version 20 and t-test was used for comparison of continuous quantitative variables (age and weight) and Chi-Square test was used to determine the qualitative relationship between variables.w Results: Out of 45,799 infants in the initial study, Blood TSH was ≥5 mIU/L in 1,241 infants (2.7%). Of these 1,241 infants, 1,159 cases (93.3%) had TSH between 5-9.9 mIU/L, 39 infants (3.1%) between 10-19.9 mIU/L, and 43 infants (3.46%) ≥20 mIU/L. The incidence of congenital hypothyroidism in the province was estimated at 1/715 live births. The mean TSH of 64 infants suffering from congenital hypothyroidism was reported 36.8±34 mIU/L (10-100). The mean age of the infants at the time of admission for second sampling was 7.5±6.5 (3-30) days. Conclusion: In view of the high incidence of congenital hypothyroidism in Hormozgan province, several times more prevalent than many areas of the world, the continuation and strengthening of the neonatal screening program appears indispensable.