Background: Maternal thyroid disease may complicate pregnancy. A high frequency of abnormal thyroid function test results in pregnant women with known thyroid disease has been reported, but the frequency of unidentified thyroid dysfunction in women first clinically diagnosed with thyroid disease after a pregnancy is not known. Methods: This was a population-based study of pregnant women in the Danish National Birth Cohort (DNBC) who had a blood sample drawn in early pregnancy and terminated the pregnancy with a singleton live-birth in the period between 1997 and 2003. Participants were all women in the DNBC who had a registration of thyroid disease before and/or up to five years after the pregnancy in nationwide health registers (n = 2445) and a 12% random sample of all women in the cohort (n = 7624). Thyrotropin and free thyroxine were measured with an immunoassay in sera stored in the Danish National Biobank. Method-and pregnancy week-specific references ranges were used for classification of thyroid function test abnormalities. Results: The frequency of abnormal thyroid function in early pregnancy was 12.5% in the random sample and 35.7% among women clinically diagnosed with thyroid disease before or after blood sampling (55.7% among women on current treatment). One third of women clinically diagnosed with thyroid disease after blood sampling had unidentified thyroid dysfunction in the early pregnancy blood sample (most frequently [52.0%] unidentified hypothyroidism in women with a later diagnosis of hypothyroidism). Conclusions: More than 50% of Danish pregnant women on current treatment for thyroid disease had thyrotropin and/or free thyroxine outside the week-specific reference ranges, and the frequency of unidentified early pregnancy thyroid dysfunction in women clinically diagnosed after the pregnancy was also high.