The findings raise concerns because thyroid hormones play a crucial role in growth and brain development in young children, health experts note.
The study by University of California, Berkeley researchers is the first to analyze the effect of bisphenol A, or BPA, on thyroid hormone levels in pregnant women and newborns.
"We are finding associations, so that is giving us concern, but I do think people need to know that we're still really learning about how BPA may impact the health of people," said Kim Harley, a study co-author and associate director of UC Berkeley's Center for Environmental Research and Children's Health.
"There's a lot more to learn, and I don't know that we have any answers yet," Harley said.
BPA has drawn increased scrutiny in recent years as the public has become aware of how easy it is to be exposed to the estrogen-like compound and how little is known about the health effects.
Studies have shown that more than 90 percent of American women of childbearing age have BPA in their urine.
The chemical is in many plastic bottles, dental sealants, resins in the lining of food and beverage cans, and some sales receipts.
Last year, California lawmakers banned manufacturers from including BPA at levels above 0.1 parts per billion in bottles or cups designed for children younger than 3, beginning July 1, 2013.
In July, the U.S. Food and Drug Administration followed suit by prohibiting the chemical in baby bottles and cups. Many manufacturers had already begun phasing out BPA in such products.
The UC Berkeley researchers analyzed BPA levels in urine samples taken from 335 mostly Latina, low-income women participating in an ongoing study in the Salinas, Calif., area.
Most of the women and their newborns had normal thyroid hormone levels, notes the study published Thursday in the journal Environmental Health Perspectives.
But for each doubling of BPA levels in some women, researchers found a corresponding decrease in one type of thyroid hormone known as T4.
They then looked at thyroid hormone levels in newborns and found the exact opposite effect - the higher the BPA level in the mother, the greater the signs of a more active thyroid in their baby boys.
No one knows why the mothers appeared to have a less active thyroid and their sons a more active one. But one theory is that the lesser amount of thyroid hormone in the mother may have caused the baby's thyroid to overcompensate, said Jonathan Chevrier, a study co-author and a UC Berkeley research epidemiologist.
It also is unclear why there appeared to be no link between a mother's BPA level and thyroid hormones in baby girls, Chevrier said.
The American Chemistry Council maintains that the weight of scientific evidence thus far is that BPA is safe. The organization also notes that BPA does not accumulate and is rapidly eliminated from the body.
If pregnant women are concerned, however, Harley notes that there are ways to reduce exposure, including buying plastic bottles that are labeled BPA free, consuming less soup, soda and other items that come in cans, declining to take receipts and washing their hands before eating if they touch a receipt.
"In general, if you can eat foods that are less heavily packaged and less heavily processed, that's probably going to lower your BPA exposure, and that's great for pregnant women anyway - eating fresh foods," Harley said.
A UC San Francisco professor, who has researched BPA but was not involved in the UC Berkeley study, called the findings intriguing and said more study is needed, including looking at the possible combined effect of BPA, flame retardants and other chemicals.
"This is one more study in the accumulating evidence that taking steps to avoid BPA would be prudent," said Tracey Woodruff, director of a UCSF program on reproductive health and the environment.
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