Objective: We aimed to compare thyroid function and cardiovascular risk factors between children conceived after in vitro fertilization (IVF) and naturally conceived children. Methods: Healthy 458 (243 boys) prepubertal children at age 6 were included. Height, body mass index (BMI), and blood pressure at resting state were measured. Thyroid function test (free T4, total T3, and TSH), fasting glucose, insulin, and lipid profiles were analyzed. Results: There were 50 IVF cases and 408 naturally conceived control children. No significant differences in height, BMI, blood pressure, fasting glucose and lipid profiles were found between two groups. IVF group showed higher TSH levels (3.2 mIU/L vs. 2.4 mIU/L, p = 0.004) and lower free T4 and total T3 levels (1.15 ng/dL vs. 1.12 ng/dL and 149.0 ng/dL vs. 142.7 ng/dL, p0.05 for both) than control group. However, differences in TSH, free T4, and total T3 levels between two groups were not significant, after adjusting for age, sex, prematurity, birth weight, multiple birth, BMI z-scores, and family history of thyroid disease. Conclusions: No significant differences in thyroid function, blood pressure, fasting glucose and lipid profiles were found between children conceived after IVF and naturally conceived children, after adjusting for covariates.