Background: Neonatal screening for congenital primary hypothyroidism (CH) is mandatory in Germany but medical care thereafter remains inconsistent. Therefore, the multicentre database HypoDok was analysed to evaluate the implementation of evidence-based guidelines in the care of children with CH and to assess the number of patients in this registry of the German society of paediatric endocrinology and diabetology (DGKED).Methods: HypoDok includes the prospective documentation of 1,630 patients with CH from 50 centres in Germany and Austria. Inclusion criteria were (i) date of birth between 10/2001 and 05/2020 and (ii) increased TSH at screening and/or confirmation. Parameters regarding diagnosis, therapy and follow-up were extracted. The number of registered patients was compared to the number in the report of the German Society for Neonatal Screening (DGNS). The cohort was divided into 2 groups, before (A) and after (B) guideline publication in 02/2011, to assess guideline’s influence on medical care.Results: 659 patients (62% female) were eligible and analysed as group A (n=327) and group B (n=332) representing 17.5% and 6.7% of CH patients identified in the German and Austrian neonatal screening program during the respective time period. Treatment start and thyroxin doses were similar in both groups and consistent with recommendations. Regular follow-ups were documented in both groups including five appointments in the first and three in the second year of life. Ultrasound of the thyroid gland was performed in 92.6% (A) and 92.1% (B) of the patients. In the first three years of life, 46.4% (A) and 40.0% (B) of the patients underwent audiometry, EQ/IQ testing was performed in 49.3% (A) and 24.8% (B) (p<0.01), respectively.Summary: While documentation of care for patients with CH by paediatric endocrinologists seems to be established, only a minority of all affected patients is included in HypoDok. Thus, the care and outcome of the majority of patients with CH remains uncertain. Therefore, comprehensive documentation as an important instrument of quality assurance and evidence-based medicine should be legally enforced and officially funded in order to record, comprehend and optimize care and outcome in patients with rare diseases such as CH, irrespective of treatment provider.