Prior to 2012 whether IVF was associated with a higher incident of birth defects was controversial. In 2012, a study was released demonstrating there is indeed a higher incidence of birth defects reported in children born by IVF compared to those born by natural conception. In 2016 another study has been published coming to the same conclusion. Now those who promote IVF, instead of questioning its association with birth defects, focus on the relatively low incidence of defects.
Below is an excerpt on this issue from the IVF chapter in my book, questioning medical technologies.
The IVF complications of twin pregnancies and of ectopic pregnancies have long been accepted. Now the evidence, that IVF is associated with a number of other increased complications to the mother and to the baby, is growing. In March 2011 the Wikipedia entry for IVF, under the heading “Complications” included the problems associated with multiple births (twins, triplets). It was easy to find evidence for problems with multiple births. The issue of other birth defects was said to be controversial. They cited a review that suggested defects were not increased and they had two citations suggesting that they were increased. One was a 2008 analysis of the data of the National Birth Defect Study in the US that found certain defects more common, including septal heart defects, cleft lip, esophageal atresia and anorectal atresia.  Some might argue that this analysis was not designed specifically to look at birth defects in IVF and thus lacked power. The second was said to be a 2002 study reviewing the birth defect record of all the IVF babies in Western Australia found that IVF kids were twice as likely to have birth defects as normal birth, where they controlled for multiple births (twins), as multiple births, independent of IVF could account for birth defects. Defects found to be more common included, heart defects, chromosomal abnormalities like Down Syndrome, gastro-intestinal abnormalities, musculo-skeletal, dislocated hips, and club feet. There was also lower birth weights, pre-term births and cerebral palsy. Unfortunately the Wikipedia site did not cite a study but a news commentary, News commentaries, from the point of view of evidence, are not very powerful. At that time I looked for compelling evidence for IVF causing birth defects and found hints at it but nothing absolutely convincing. Now in January 2012 the Wikipedia site has evolved and it no longer says that the association of IVF with birth defects is controversial. Now they cite a 2012 systematic review and meta-analysis of obstetric and neonatal outcomes in singleton IVF pregnancies. By looking at singleton births (only one baby) only they exclude the added risk associated with twin births. This study shows that birth defects are 1.6 times more likely in IVF birth than in normal births.  This 2012 study is more difficult to argue against. This study reviewed a number of problems that were increased as well as birth defects, including, bleeding at the time of birth, high blood pressure, premature rupture of membranes, caesarian sections, gestational diabetes, induction of labour, low birth weight babies, premature babies, and death of baby around the time of birth. The increased risks were 1.18 to 2.49 times as likely as in normal births. Now, in 2016, another study also demonstrates a similar increase in birth defects in IVF births.
One can argue that these risks are low but should we be trying so hard to have babies using IVF when we know that it puts mothers and our children at increased risk?
 IVF: Questions We Should Ask, Author: Greg Kenyon
 Esophageal atresia is failure of the esophagus (the swallowing tube) to develop a passage way in it. Anal atresia is failure of the anal opening of the bowels to develop.
 Reefhuis J, Honein et al., “Assisted reproductive technology and major structural birth defects in the United States”, Human Reproduction, 24(2): 360-366.
 Jonica Newby, “IVF Defects”, Catalyst, Australian Broadcasting Corporation, https://www.abc.net.au/catalyst/stories/s904186.htm
 Pandey, S.; Shetty, A.; Hamilton, M.; Bhattacharya, S.; Maheshwari, A. (2012). “Obstetric and perinatal outcomes in singleton pregnancies resulting from IVF/ICSI: A systematic review and meta-analysis”. Human Reproduction Update 18 (5): 485–503
 Sheree L. Boulet, DrPH, MPH1; Russell S. Kirby, PhD2; Jennita Reefhuis, PhD3; Yujia Zhang, PhD1; Saswati Sunderam, PhD1; Bruce Cohen, PhD4; Dana Bernson, MPH4; Glenn Copeland, MBA5; Marie A. Bailey, MA, MSW6; Denise J. Jamieson, MD, MPH1; Dmitry M. Kissin, MD, MPH; for the States Monitoring Assisted Reproductive Technology (SMART) Collaborative1, “Assisted Reproductive Technology and Birth Defects Among Liveborn Infants in Florida, Massachusetts, and Michigan, 2000-2010”. JAMA Pediatr. 2015.4934. Published online April 04, 2016. doi:10.1001/jamapediatrics.
This article can be found at https://archpedi.jamanetwork.com/article.aspx?articleid=2506140 as of July 2016.
There is a news article reporting on this study at https://www.reuters.com/article/us-health-ivf-birth-defects-idUSKCN0X122D as of July 2016