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This article contains data on the effective factors on congenital hypothyroidism (CH) that was learned from a case-control study designed in Khuzestan province in Iran. The data set of this article provides information on newborn descriptive features and effective factors on Neonatal Congenital Hypothyroidism that occurs in Khuzestan Province, Iran.Congenital Hypothyroidism is one of the most important causes of preventable mental retardation in infants, “Prevention of intellectual disability through screening for congenital hypothyroidism: how much and at what level? Archives of disease in childhood” (Grosse and Van Vliet, 2011) [1]. The prevalence of this disorder in Iran is higher than the global average, “Epidemiology of congenital hypothyroidism in Markazi Province, Iran” (Dorreh et al., 2014) [2]. The related case-control study was on the identification of effective factors on congenital hypothyroidism (CH) that designed in Khuzestan province in Iran. The understudy variables were neonatal TSH level (mu/L), birth weight (gr), age (day), to being twins, sex, parental Consanguinity, and mothers’ age.The understudy population was infants, who were under-covered by the national screening program in Khuzestan province. 183 cases and 192 controls were selected during this study. There was the significant association between Female gender [OR = 1.9(1.1–3.1)] and Twinning [OR = 4(1.8–9.7)] with CH. According to multivariate analysis results, the Relationship between Consanguinity and CH was not statistically significant [OR = 1.2 (0.7–1.8)]. Keywords: Congenital hypothyroidism, Risk factors, Khuzestan