Objective To evaluate the newborn screening programme for congenital hypothyroidism (CH) in Iran from diagnosis to management and follow-up for 3 years from 2011 to 2014.

Design Retrospective cohort.

Setting and patients Seventeen university districts were randomly selected from 30 provinces. Central data in each district were gathered and collectively analysed. Congenital hypothyroid subjects were followed for 3 years.

Main outcome measures Programme coverage, screening and treatment age, recall rate, compliance to follow-ups.

Results The total number of births in 2011 was 501 726, of which 452 918 neonates (90.3%) were screened and 15 671 (3.46%) were recalled; 1085 (1:462, 0.22%) were confirmed as having CH (57.1%: permanent, 42.9%: transient) and followed for 3 years. Positive predictive value (PPV) for the first screening test was 6.9%. After the second screening, recall rate was reduced to 0.69% and PPV increased to 31.3%. Median age at screening was 6 (3–9) days and for 90.6% of patients treatment was initiated before 40 days of age with a median levothyroxine dosage of 25 µg/day; 131 (13.4%) were lost to follow-up. Mean number of follow-up visits over 3 years was 5.7 (95% CI 5.5 to 5.9) and 23% (n=225) had total compliance to all follow-ups. Median time for thyroid stimulating hormone normalisation was 45 days, 95% CI (41.1 to 48.8).

Conclusion In Iran, despite well-established protocols of screening and detecting CH subjects, stricter implementation of a structured system for monitoring and surveillance is needed to promote the management of patients and to reduce rates of loss to follow-up. Determining and addressing the causes of high false positive rates must be prioritised.