A new study shows that women who take antidepressants in the later stages of pregnancy are more likely to have a child with autism.

The study specifies one particular group of antidepressants in particular — the SSRIs, or selective serotonin reuptake inhibitors, such as Prozac, Zoloft or Paxil.

“Use of antidepressants, specifically selective serotonin reuptake inhibitors, during the second and/or third trimester increases the risk of autism spectrum disease in children, even after considering maternal depression,” Anick Berard of the University of Montreal and colleagues wrote in their report.

Doctors say they are worried the findings will scare many women into stopping antidepressants, but experts were quick to note that the absolute risk is very small and very few children were diagnosed with autism.

“If articles like this make people come off medication that they need to function, that’s terrible for society."

Berard’s team studied more than 145,000 children born in Quebec between 1998 and 2009. They found 4,700 babies, or 3 percent of the total group, whose mothers took some type of antidepressant while pregnant.

Only 31 babies, or 1 percent of the group whose mothers took antidepressants in later pregnancy, were later diagnosed with autism.

However, those babies were more likely to have been born to mothers who took antidepressants in the second or third trimester of pregnancy, they reported in the Journal of the American Medical Association’s JAMA Pediatrics. More careful analysis showed it was only the SSRIs.

“Other classes of antidepressants were not statistically significantly associated with an increased risk of autism spectrum disorder,” they wrote.

Dr. Eva Pressman, who chairs the department of Obstetrics and Gynecology at the University of Rochester in New York, says the study raises more questions than it answers.

“If there is an effect that SSRIs have on autism, I think it is not a very large effect,” she told NBC News.

Pressman, who has prescribed SSRIs to pregnant women herself, said it’s a judgment call. In general, pregnant women should take as few medications as possible, she said.

“If the patient can be safely managed without medication, that’s always in their interest,” she said. “In some patients, the depression is clearly more dangerous than the medication.”

And it’s dangerous for anyone to suddenly stop taking antidepressants. “If articles like this make people come off medication that they need to function, that’s terrible for society,” said Pressman, who was not involved in the study.

Antidepressants are very widely used in the U.S. and 13 percent of U.S. women took them while pregnant in 2003, the researchers said. That's up from 5.7 percent in 1999. In Canada, 4.5 percent of pregnant women took them between 2001 and 2006.

What the study cannot show is why there was a higher risk in some women. Women who continue to take antidepressants during pregnancy may be more severely depressed than women who do not take them, and that itself may change their child’s risk. Depression and autism both have a very strong genetic roots.

“For example women who took antidepressants were more likely to have a history of psychiatric and other illness, were older, and we're more likely to have had another child with autism,” said Dr. Gail Saltz, a psychiatrist at The New York Presbyterian Hospital Weill-Cornell School of Medicine.

“Each of these factors could increase the risk of autism. So the study says there was a difference but can't say if the drug caused the difference or whether these differences are what increased the risk.”

The researchers note other studies have shown there could be a biological basis for SSRIs affecting a child’s brain, however. “Selective serotonin reuptake inhibitors cross the placenta and are found in amniotic fluid,” they said.

“The circulating neurotransmitters may be different in someone with depression, or someone with severe depression.”

Serotonin is a message-carrying chemical called a neurotransmitter and it’s linked with mood, but it performs other important functions, too. “We know that all neurotransmitters play a role in not only sending signals but how the brain reacts to those signals and how the brain develops,” Pressman said.

“The circulating neurotransmitters may be different in someone with depression, or someone with severe depression.”

So, in other words, it’s complicated. Autism is almost certainly caused by a combination of genetics and so-called external influences such as what happens in the womb and perhaps in infancy too, experts say. Studies show when women get the flu while pregnant, for instance, it may raise the risk of autism.

And other studies done looking specifically at antidepressants in pregnancy have had mixed results. One published in June this year found that it seemed to be the mother’s degree of depression, and not the antidepressants, that was most strongly associated with a child’s autism.

Autism diagnoses are on the rise in the U.S. The latest study finds one in 45 U.S. kids have been diagnosed with an autism spectrum disorder.