Abstract Background: We investigated the relationship between iodine status and thyroid function in children with congenital hypothyroidism (CH) with eutopic gland. We also evaluated whether the presence of iodine organification defect (IOD) or pathogenic genetic variants affects the association between iodine status and thyroid function. Methods: A total of 31 children (14 boys) with CH participated in the study, who repeatedly underwent thyroid function test and urine iodine concentration (UIC) without levothyroxine (LT4) medication after 3 years of age (1-5 times per patient). After confirming eutopic gland, IOD was demonstrated by the positive perchlorate discharge test with a discharge rate >10%. Genetic analysis was performed using targeted gene sequencing including 23 genes. Results: We identified likely pathogenic or pathogenic variants in 14 cases (45.2%): 1 case with triallelic (digenic) variants (DUOX2 and TSHR), 4 cases with biallelic variants (3 DUOX2 and 1 TSHR), and 9 cases with monoallelic variants (7 DUOX2, 1 DUOXA2, and 1 TSHR). Among 26 cases treated with LT4 from neonatal period, thyroid function after LT4 discontinuation was euthyroid (n = 7), subclinically hypothyroid (n=15), and overtly hypothyroid requiring LT4 (n = 3). The other 5 cases without LT4 treatment remained subclinical hypothyroid. After excluding 2 cases with TSHR, 29 cases (with 72 samples) were included to analyze the relationship between iodine status and log-transformed TSH (log-TSH) using generalized estimating equation models. The positive IOD (n = 17) was not associated with presence of DUOX2/DUOXA2 variants (n = 12). Iodine status of urine samples was categorized into adequate (UIC < 300 μg/L, n = 25), mild excessive (UIC = 300-599 μg/L, n = 14), and severe excessive (UIC ≥ 600 μg/L, n = 33) groups. When stratified by the presence of IOD, log-TSH significantly increased in severe excessive group (β = 0.52, P = 0.014 vs. iodine adequate group) among negative IOD group, but rather decreased in mild excessive group (β = -0.84, P < 0.001 vs. iodine adequate group) among positive IOD group. Meanwhile, when stratified by the presence of DUOX2/DUOXA2 variants, no significant association was found between iodine status and log-TSH levels. Conclusion:DUOX2 mutation was most common in CH patients with eutopic gland. The relationship of iodine status with thyroid function differed by presence of IOD.