A large number of congenital hypothyroidism (CH) cases in Iran are transient. This study was designed to investigate the aetiology of permanent CH (PCH) by thyroid scintigraphy (TS) and its relationship with the first diagnostic thyrotropin (TSH). During 12 years (2005-2017) of CH screening in southwest Iran, all infants referred with the diagnosis of CH were followed until their third birthday, when they were re-evaluated for serum T4, TSH after discontinuing the treatment for 3-4 weeks. If the last test indicated a PCH state (TSH >10 mU/L with any levels of T4), TS was performed, and, based on the results, the patients were categorised as agenesis, dysgenesis (sublingual, thyroglossal cyst), and normal/diffuse goitre (indicating dyshormonogenesis). After excluding all transient CH subjects, 224 permanent CH cases were enrolled (52.7% female). Seasonal distributions were as follows: spring: 25.7%, summer: 27.9%, autumn: 20.3%, and winter: 26.1%. No significant differences were found between females and males and the different modes of delivery (55.4% were delivered by caesarean section) regarding T4, TSH (p > 0.05). Of a total of 213 performed scans, 20.7% had agenesis, 36.2% had dysgenesis, and 43.2% were normal or goitrous. Those with agenesis/dysgenetic thyroid had a lower T4 and a higher TSH than those with normal scans. However, the differences were not significant. Compared to those who had TSH < 40 mU/L, patients with TSH ≥ 40mU/L had 46% (95% CI: 1.06-2.02) more risk of agenesis or dysgenesis in TS. More than 40% of PCH are caused by dyshormonogenesis in Iran. Having a TSH ≥ 40 mU/L after the first week of life significantly raises the probability of thyroid agenesis/dysgenesis as the cause.