Background/Purpose: This study aims to establish reference intervals for important biochemical parameters in cord blood of newborn male and female infants in Taiwan and to investigate their sex difference. We also examined the correlation of the same markers between maternal blood levels and neonatal cord blood levels. Methods: 2,136 pregnant women receiving regular routine prenatal health assessments in their third trimester (weeks 29–40) were recruited from nine hospitals in Taiwan between 2012 and 2015. After exclusion, we were left with 580 cord blood samples to include in this study. Results: Cord blood thyroid-stimulating hormone was higher in males than females (p < 0.05). Males also had significantly higher sex hormone levels (estradiol, follicle-stimulating hormone, and sex hormone-binding globulin), while females had higher levels of luteinizing hormone. Male newborns had higher cord blood immunoglobulin E (IgE), while females had higher insulin-like growth factor-1 (IGF-1) levels. We found a slight positive link between maternal blood and cord blood in thyroid hormones and sex hormones. Conclusion: This study found sex differences in cord blood thyroid hormone, sex hormone, IGF-1, and IgE levels and a link between maternal blood levels of thyroid and sex hormones and those in the cord blood of their infants.