Abstract Background Neonatal Thyroid Stimulating Hormone (nTSH) is proposed as indicator of iodine deficiency in a population. Population’s iodine sufficiency is indicated by a proportion of the newborns less than 3% having nTSH above 5 mIU/L. The aim of this study was to explore the Dutch neonatal heel prick screening TSH data to assess iodine status in the Netherlands and identify determinants and potential confounders of this assessment. Methods All newborns born in the Netherlands between 2007 and 2015 with a heel prick collection at day 3-7 were included ( n = 1,435,600), except preterm neonates and baby’s with a low birth weight. Total T4 was measured for all children, nTSH was measured in the ~ 20% children with lowest total T4. Results The proportion with nTSH > 5mIU/L fluctuated between 0.6-1.3% in 2007-2015. nTSH was significantly associated with laboratory performing the nTSH assay and age of heel prick sampling. The overall increasing trend in proportion nTSH >1mIU/L was confounded by the laboratories with different and changed assays. Conclusions The low proportion neonates with high nTSH suggests a sufficient iodine status in the Netherlands. Whether the increased proportion nTSH>1mIU/L over the years is an early indicator of deterioration of the iodine status remains unclear, due to differences and changes in analytical assays. nTSH might be a valuable and inexpensive way to get crude insight in the (trend in) iodine status, but more research is needed on the validity and potential conditions.