Maternal smoking was associated with a subsequent decreased risk of developing hypothyroidism (adjusted HR 0.75 (95% CI 0.70-0.81)) and an increased risk of hyperthyroidism (1.38 (1.27-1.49)). Danish nationwide registration of maternal smoking during pregnancy adds further evidence to an association between smoking and thyroid dysfunction; smoking reduced the risk of hypothyroidism and increased the risk of hyperthyroidism.