BACKGROUND: Perfluoroalkyl and polyfluoroalkyl substances (PFAS) have been reported to disrupt the thyroid function. But epidemiological evidence on the association between PFAS and thyroid hormone (TH) levels in cord blood is scarce and controversial. We aimed to examine the association between cord blood PFAS concentrations and TH levels in prelabor caesarean deliveries. METHODS: We measured ten PFAS and three THs in cord blood in 568 prelabor caesarean deliveries. The associations between PFAS and TH levels were examined using multiple linear regression model and sparse partial least squares (SPLS) regression model. RESULTS: In SPLS analyses, thyroid stimulating hormone (TSH) level decreased with increasing concentrations of perfluorooctane sulfonate (PFOS, β = -0.012, 95% confidence interval [CI]: -0.019, -0.005), perfluorononanoic acid (PFNA, β = -0.012, 95% CI: -0.019, -0.005), perfluorodecanoic acid (PFDA, β = -0.012, 95% CI: -0.02, -0.005), perfluoroundecanoic acid (PFUA, β = -0.013, 95% CI: -0.021, -0.006) and perfluorododecanoic acid (PFDoA, β = -0.013, 95% CI: -0.023, -0.006). Moreover, we found a positive association between PFDoA and free thyroxine (FT4) levels (β = 0.190, 95% CI: 0.063, 0.304) after adjusting for potential confounders. Free tri-iodothyronine (FT3) levels were positively associated with concentrations of PFOS (β = 0.059, 95% CI: 0.023, 0.100), but negatively associated with PFDoA (β = -0.153, 95% CI: -0.212, -0.106). We also observed gender disparity in the associations of PFAS exposure and FT3, FT4, TSH levels. CONCLUSION: Our results suggest that prenatal exposure to certain PFAS may disrupt fetal thyroid function. The effect may be gender-specific.