Subtypes of primary congenital hypothyroidism (CHT) showed different degrees of impairment of thyroid function at screening and confirmation. Patients with athyrosis showed the greatest impairment with mean value for screening 1-thyroxine (ScrT4) of 2.73 micrograms/dl (p < 0.0001 vs E group), screening thyroid-stimulating hormone (ScrTSH) of 327.6 microIU/ml (p < 0.0001 vs E group), confirmatory L-thyroxine (ConT4) of 1.21 micrograms/dl (p < 0.0001 vs E group), and confirmatory thyroid-stimulating hormone (ConTSH) of 572 microIU/ml (p < 0.0001 vs E group). Infants with dysgenetic ectopic thyroids (E group) showed the best preservation of function with mean values for ScrT4 of 6.0 micrograms/dl, ScrTSH of 229 microIU/ml, ConT4 of 6.23 micrograms/dl, and ConTSH of 324.8 microIU/ml. Generally, intermediate mean values were found for infants with normal or goitrous thyroids with values for ScrT4 of 4.26 micrograms/dl, ScrTSH of 205 microIU/ml, ConT4 of 3.21 micrograms/dl, and ConTSH of 428 microIU/ml. The risk for CHT being missed appeared to be greatest in patients with dysgenetic ectopic thyroids with the mean difference between ScrT4 and the L-thyroxine cutoff value (ScrT4Diff) being -2.2 micrograms/dl; five cases fell within 0.5 microgram/dl of the cutoff. The risk was least in infants with athyrosis with ScrT4Diff of -4.64 micrograms/dl (p < 0.0001 vs E group); no cases were within 1 microgram/dl of missing the cutoff. For infants with normal or goitrous thyroids ScrT4Diff was -3.44 micrograms/dl; one case was initially missed and three fell within 0.5 microgram/dl of the cutoff. The risk for missing CHT in screening is apparent. Clinical vigilance must be maintained to detect missed cases as early as possible.