Introduction: Congenital hypothyroidism (CH) is one of the most common endocrine and metabolism diseases and also one of the common curable factors of physical growth and mental disabilities disorders. The prevalence of congenital hypothyroidism is 1 in 3000 to 1 in 4000 of live births in the world and about 1 in 670 live births in Iran. This situation may be transient or permanent. Postponing diagnosis and treatment of congenital hypothyroidism even for 3 months after birth lead to loss of IQ by 50 percent. However, the diagnosis and treatment of this disease is very easy. The purpose of current study is to survey the prevalence level of congenital hypothyroidism kinds and related factors in children of Kurdistan Provinces in 2005 to 2011 and acquiring the information necessary to chart the disease and designing preventive measures at the first and second levels. Materials and Methods: This is a descriptive-analytic study and that was conducted cross-sectional on all neonates with congenital hypothyroidism in Kurdistan province during 2005-2007. The affected infants with congenital hypothyroidism from the cities of Kurdistan province have been selected according to the form of care for congenital hypothyroid patients who were provided by health centers of the province between 2005 and 1390. The form for all patients after initial positive screening and confirmation of diagnosis was provided and delivered to the provincial health center. After collecting data, they were analyzed by inputting into SPSS software. Results: The number of patients was included of 279 boys (59%) and 188 girls (41%). The illness prevalence in boys, girls and total was 1 in 293, 1 in 418 and 1 in 344 in newborn infants, respectively. According to the findings, the incidence of transient congenital hypothyroidism was 1 in 446 and the prevalence of persistent type 1 in 1515 newborns. Data analysis indicated that the prevalence of congenital hypothyroidism in males was 48 percent and 1 fold and there was a significant relationship between type of hypothyroidism and gender (P = 0.000). Also according to the results of familial marriages, there is a significant relationship with the increase in chronic hypothyroidism in Kurdistan province and also there was a significant relationship between the type of hypothyroidism and parental relationship (P = 0.000). Conclusion: The prevalence of congenital hypothyroidism in Kurdistan province is higher than the national average and multiplied by the average of countries with a screening program. Hence, this disease is of particular importance and people's awareness and the health care staffs are necessary in order to raise awareness about the irreversible complications of the disease in the absence of treatment. On the other hand, supplementary studies to clarify the relevant factors, especially iodine deficiency and family marriage, are the research priorities of the health system in the province.