Clomid has the highest risk of birth defects out of all the fertility treatment methods. Clomid stops the growth of new blood vessels which can lead to abnormalities. There is a chance that a baby conceived through this method might develop some irregularities such as anencephaly (unfinished brain and skull), contraction of the aorta, craniosynostosis (premature fusion of skull), oesophagus atresia ( part of oesophagus missing at birth), omphalocele (abdominal organs are outside the body), and septal heart defect ( hole in the wall of the heart).