However, the researchers said they did not know if the birth defects were caused by the antibiotics or the underlying infection.
One expert said women need to remember the good antibiotics can do mom and baby, as well. Though many pregnant women want to avoid taking any drugs during pregnancy, infections pose a risk to mother and baby and often need to be treated, said Dr. Jennifer Wu, an obstetrician-gynecologist at Lenox Hill Hospital in New York City.
"Untreated infections during pregnancy can lead to severe consequences, such as maternal sepsis [blood infection] and preterm labor," Wu said. "Yet many patients are afraid to take medications such as antibiotics during pregnancy."
The study "supports the evidence that antibiotics are safe for pregnant women," she said. "It is reassuring for doctors and patients to have more data on necessary drugs for pregnancy."
Crider also stressed that the chances of having a baby with a birth defect remain small, even if an antibiotic has been linked to an elevated risk. For example, the risk of having a child with hypoplastic left heart syndrome is about one in 4,200. Sulfonamides were associated with a three-fold increase, making the likelihood about one in 1,400, she said.
Brand names for nitrofurantoins include Furadantin, Macrobid and Macrodantin. Bactrim and Septra are among the brand names of sulfonamides.
Given the data, Crider said, women should be cautious about taking either of those types of drugs during pregnancy and should discuss other options with their physicians,.
According to the study, the overall risk for having a child with a birth defect is about three percent.
The study did not look at chromosomal defects, including Down syndrome.
The U.S. Centers for Disease Control and Prevention has more on birth defects.
SOURCES: Krista Crider, Ph.D., geneticist, National Center on Birth Defects and Developmental Disabilities, U.S. Centers for Disease Control and Prevention, Atlanta; Jennifer Wu, M.D., obstetrician-gynecologist, Lenox Hill Hospital, New York City; November 2009, Archives of Pediatrics & Adolescent Medicine