Aims: To evaluate therapy and dose adjustments in patients with congenital hypothyroidism (CH), longitudinally followed up until 16 years old, according to aetiology, Beclard’s nuclei presence, and thyroxine (T4) level at diagnosis. Methods:L-T4/kg/day and dose change ratio (CR) were assessed in 74 CH patients. Results: The dose was statistically larger in athyreosis than in dyshormonogenesis (1–10 and beyond 14 years) and in ectopy (2, 15, 16 years). The ectopic children required statistically larger L-T4/kg than the dyshormonogenetic ones (3–7 years). The L-T4/kg/day was increased, not statistically, in patients or with T4 <30 nmol/l or without Beclard’s nuclei at diagnosis. The CR progressively dropped after the 6th month at each attendance, without any difference in terms of aetiology, T4 level at diagnosis, or Beclard’s nuclei. The total CR was greater (significantly) in patients without Beclard’s nuclei, and (not significantly) in those with T4 <30 nmol/l at diagnosis or with agenesia. Conclusion: The L-T4 dose in CH is highly affected by the aetiology. The CR is higher in patients with delayed bone maturation at diagnosis. We suggest that these latter patients need blood tests more frequently to obtain a proper titration of the therapy.