While the results of animal studies have shown that perfluorinated compounds (PFCs) can modulate concentrations of thyroid hormones in blood, limited information is available on relationships between concentrations of PFCs in human blood serum and fetal thyroid hormones. The relationship between concentrations of PFCs in blood and fetal thyroid hormone concentrations or birth weight, and ratios of major PFCs between maternal and fetal serum were determined. Concentrations of PFCs were measured in blood serum of pregnant women (n = 44), fetal cord blood serum (n = 43) and breast milk (n = 35). Total concentrations of thyroxin (T4), triiodothyronin (T3) and thyroid stimulating hormone (TSH) in blood serum were also quantified. The ratios of major PFCs in maternal versus fetal serum were 1:1.93, 1.02, 0.72, and 0.48 for perfluorotridecanoic acid (PFTrDA), perfluorooctanoic acid (PFOA), perfluorohexane sulfonate (PFHxS), and perfluorooctane sulfonate (PFOS), respectively. Fetal PFOS, PFOA, PFTrDA and maternal PFTrDA were correlated with fetal total T4 concentrations, but after adjusting for major covariates, most of the relationships were no longer statistically significant. However, the significant negative correlations between maternal PFOS and fetal T3, and maternal PFTrDA and fetal T4 and T3 remained. Since thyroid hormones are crucial in the early development of the fetus, its clinical implication should be evaluated. Given the observed trans-placental transfer of PFCs, efforts should be also made to elucidate the exposure sources among pregnant women.