PURPOSE: The function of the neonatal thyroid is affected transiently or consistently by various maternal thyroid diseases, neonatal diseases, drugs, and more as well as thyroid dysgenesis. In this study, we analyzed several factors of neonatal thyroid dysfunction through neonatal screening test and investigated the prognosis. METHODS: From January 1992 to July 1997, we reviewed 66 newborn patients, who showed abnormal thyroid function in neonatal screening test, and analyzed 62 cases except for 3 cases of thyroid dysgenesis and 1 case of TBG deficiency. In the end, we statistically compared the maternal thyroid disease group with umbilical-iodinated disinfection group because the other groups were too small in numbers. RESULTS: Among 62 cases of neonatal thyroid dysfunction, maternal thyroid disease (A) group had 29 cases (46.8%), umbilical-iodinated disinfection (B) group had 22 cases (35.5%), neonatal disease (C) group had 7 cases (11.2%), idiopathic (D) group had 4 cases (6.4%). Group A showed compensated hypothyroidism 79.3%, transient hypothyroidism 13.8% and hyperthyroidism 6.9%, while group B showed compensated hypothyroidism 77.3% and transient hypothyroidism 22.7%. Capillary TSH showed that group B was significantly higher than group A (P<0.05). The serum T4 showed that group B was significantly lower than group A (P<0.05). The incidence of medication showed no significant difference between groups A and B. The duration of normalizing thyroid function showed that group B was significantly longer than group A. CONCLUSOIN: The iodide-containing disinfectant caused transient thyroid dysfunction which was longer and more severe than in the maternal thyroid disease group even though the time of causative exposure differed.