Maternal urinary iodine concentration (UIC) and blood neonatal thyroid stimulating hormone (TSH) concentration reflect iodine status in pregnancy. As dietary measures in gestational diabetes mellitus (GDM) could affect iodine intake, our study aimed to investigate iodine supply in women with GDM compared to healthy pregnant women and to evaluate its relationship to thyroid function. UIC and serum TSH, free thyroxine (FT4) and autoantibodies against thyroid peroxidase (TPOAb) were analysed in 195 women with GDM and 88 healthy pregnant women in the 2nd trimester. Subsequently, neonatal TSH concentrations measured 72 hours after delivery in a subgroup of 154 newborns (115 of mothers with GDM and 39 controls) from the national register were analysed. Optimal iodine intake was found only in nine women with GDM (4.6%) and 33 healthy pregnant women (37.5%) (P<0.001). Most pregnant women with GDM (88.7%) as compared to one half of controls (50%) had iodine deficiency (P<0.001). Also, hypothyroxinaemia was more prevalent in GDM compared to controls (12.3% vs 3.4%, P = 0.032). Consistently, neonatal TSH >5.0 mIU/L indicating iodine deficiency was found in 6 (5.2%) newborns of women with GDM as compared to none in controls. In the multiple logistic and linear regression models in women with GDM, hypothyroxinaemia was associated with preterm births, and a negative association of serum FT4 and HbA1c was found. Iodine deficiency in pregnancy was more prevalent among women with GDM compared to healthy pregnant controls. Hypothyroxinaemia was associated with preterm births in women with GDM.