It’s probably safe for mothers to get the H1N1 flu vaccine in their first trimester of pregnancy, according to a new study published in the journal Annals of Internal Medicine.

Researchers did not see a direct link between the vaccine and overall congenital malformation in offspring. Previously, this risk was poorly understood, according to the study authors.

The study was the first to look at the potential for congenital malformation associated with H1N1 vaccines during early pregnancy, with the results controlling for confounding factors such as familial risk for such abnormalities.

The study focused on the GlaxoSmithKline vaccine called Pandemrix administered to nearly 138,000 pregnant women in Sweden during the 2009 and 2010 H1N1 pandemic. The researchers measured the other usual covariates such as maternal age, weight and smoking habits. But with Sweden’s comprehensive national health records, they were also able to include information on the resulting babies’ siblings’ health in order to control for potential familial conditions confounding the vaccine data.

The 137,66 women included in the study gave birth to 238,571 babies. They included about 41,000 fetuses that were exposed to Pandemrix during pregnancy (about 14,000 of which were exposed in the first trimester) and about 198,000 babies who were not prenatally exposed to the vaccine.

About 4.97 percent of the exposed babies and 4.78 percent of the unexposed babies developed congenital malformations that were recorded within the first years of their births. After adjusting for the confounding factors, the researchers determined that risk for a congenital malformation after a Pandemrix vaccine was about 4.98 percent. With no vaccine, the risk was about 4.96 percent—meaning that an H1N1 vaccine during pregnancy increased offsprings’ risk of a congenital malformation by about .02 percent. The risks were slightly higher in the first trimester and the first eight weeks of pregnancy—about 0.16 percent higher and 0.1 percent higher than unexposed babies, respectively.

The study authors pointed out that even though overall risk of congenital malformation were not significantly higher among the exposed population, it’s still possible the risk for specific malformations (such as congenital heart disease, oral cleft or limb deficiency) increased with the vaccinated population. The incidence numbers for each of those specific problems were too small to come to a definitive conclusion, the researchers pointed out.

Understanding the risk for such issues could be important for patients and doctors as they weigh those risks against the potential risks to women and their fetuses of contracting an influenza infection while pregnant.