It’s such an important question but answering that question is not simple.
Although most pregnancies conceived by IVF have healthy outcomes, there have been some reports of increased risk for birth defects in babies conceived with IVF. However, these studies and findings have not been consistent. In 2016, CDC used national ART surveillance data linked with information from vital records and birth defects registries for three states (Florida, Massachusetts, and Michigan), and studied ART and birth defects in 4 million infants. Data from this large population showed that, if we don’t look at congenital anomalies that are associated with abnormal chromosomes (for example Down's Syndrome), the overall chance of having non-chromosomal defects was 5.8% per 1000 for ART infant, which is slightly higher than 4.7 per 1000 for non-ART infants. Babies conceived using ART were more likely to have congenital defects such as cleft lip, cleft palate or a congenital heart defect. In addition to the structural birth defects, some evidence links IVF to two genetic diseases: Beckwith-Weidemann syndrome and Angelman syndrome. However, whether these outcomes are due to the ART treatment or whether it is due to the inherent problem that has led to the couple being unable to conceive naturally and having to use ART is unclear. Also, we have to remember that the absolute risk of having these defects are very low. For example, even IVF babies have ten times higher chance to have Beckwith-Wiedemann syndrome or Angelman syndrome, that chance would still be 1 in 1300 or 1 in 1000. Of course all these findings deserve more research attention, but based on observed data, IVF is considered safe and does not have much greater risks than those of natural conceptions.