Objective: Thyroid disorders and iron deficiency (ID) are associated with obstetrical and fetal complications. Iron is essential for the normal functioning of thyroid peroxidase (TPO-abs) and ID is frequent during pregnancy. The aim of this study was to compare the prevalence of thyroid autoimmunity (TAI) and dysfunction during the first trimester of pregnancy in women with and without ID. Design: Cross-sectional data analysis of 1900 pregnant women nested within an ongoing prospective collection of pregnant women's data. Method: The study was performed in a single, tertiary referral center. During the first antenatal visit, ferritin, TPO-abs, thyroid-stimulating hormone (TSH) and free T 4 (FT 4 ) were measured and age and BMI were recorded. ID was defined as ferritin <15 µg/L, TAI when TPO-abs was >60 kIU/L, and subclinical hypothyroidism (SCH) when TSH was >2.5 mIU/L. Results: ID was present in 35% of women. Age and BMI were comparable between both groups. In the ID group, the prevalence of TAI and SCH was significantly higher, compared with that in the non-ID group (10% vs 6% and 20% vs 16%; P = 0.011 and 0.049 respectively). Ferritin was inversely correlated with serum TSH (ρ = −0.076; P = 0.001) and positive with FT 4 levels (ρ = 0.112; P < 0.001). In the logistic regression model, ID remained associated with TAI after correction for confounding factors (P = 0.017). The association with SCH was absent after correction for the confounders in the logistic regression model (P = 0.082), but remained present in the linear regression model (P = 0.035). Conclusions: ID was frequent during the first trimester of pregnancy and was associated with a higher prevalence of TAI, higher serum TSH, and lower FT 4 levels.