Researchers found that despite increasing use of IVF in the US, associations between birth defects and IVF are poorly understood.
Management of birth defects comprises a large part of pediatric surgical care and demands significant health care resources.
Researchers examined infants born in California from 2006-2007 after IVF and other treatments such as fertility-enhancing drugs or artificial insemination.
They examined maternal age, race, the number of times the mother had given birth, infant gender, year of birth and presence of major birth defects.
"Our findings included a significant association between the use of assisted reproductive technology, such as certain types of in vitro fertilisation, and an increased risk of birth defects," said study author Lorraine Kelley-Quon, a general surgery resident at Ronald Reagan UCLA Medical Center.
Overall, 3,463 infants with major birth defects were identified among 4,795 infants born after IVF and 46,025 naturally conceived infants with similar maternal demographics.
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Birth defects were significantly increased for infants born after IVF, 9 per cent versus 6.6 per cent for naturally conceived infants, even after controlling for maternal factors.
Specifically, malformations of the eye (0.3 per cent versus 0.2 per cent), heart (5 per cent versus 3 per cent), and genitourinary system (1.5 per cent versus 1 per cent) were greater in IVF infants.
An IVF infant's odds of birth defects were 1.25 times greater than that of a naturally conceived infant with similar maternal characteristics. Risk of birth defects after other fertility treatments such as artificial insemination or ovulation induction alone were not significant.
"For parents considering in vitro fertilisation or other forms of assisted reproductive technology, it is important that they understand and discuss with their doctor the potential risks of the procedure before making a decision," said Kelley-Quon in a statement.