Background: Congenital hypothyroidism (CH) is the most common endocrine diseases and one of the major causes of preventable mental retardation. This study was conducted to investigate the prevalence of transient and permanent congenital hypothyroidism in Kurdistan province, Iran. Materials and Methods: In this cross-sectional study, all registered congenital hypothyroidism neonate of health centers of cities covered by Kurdistan University of Medical Sciences during 2006 to 2014 entered to study. Demographic and laboratory information of CH neonates was collected and entered into the Stata-12 and was analyzed using student t-test and Chi-square statistic and P-value less than 0.05 was considered. Results: Overall incidence rate during 2006 to 2014 for province was 1.8, 2.3, 3.2, 4.3, 3.3, 4.0, 3.6, 4.6 and 2.7, respectively per 1000 neonates in this period. The number of diagnosed patients was 855 cases including 519 (60.7%) boys and 336 (39.3%) girls who 516 (60.4%) cases were from urban areas. Of the total patients, 202 (22.6%) were permanent. There was no significant difference between gender, location, type of childbirth, and season of birth with transient and permanent types of disease (P. 0.05); while, there was a significant statistical relationship between consanguineous marriages and congenital hypothyroidism (P< 0.05). Conclusion: The prevalence of congenital hypothyroidism in Kurdistan province is significantly higher than the global and country levels that emphasize the continuation and reinforcement of screening program of infants. Therefore, complementary studies are research priorities of the health system in Kurdistan province in order to clarify the environmental and genetic factors related.