What are the chances that the fetus will be malformed if you have an ongoing pregnancy?
If you have an ongoing pregnancy after using Misoprostol, the risk of having a baby with fetal malformations is increased. However, this risk is very small, less than 1 in 1000. This risk is smaller than the normal risk of having a baby with Down Syndrome.
This very small risk does not exist when a woman has taken Misoprostol after the 12th week of her pregnancy!
If possible, we advise women with ongoing pregnancies to undergo surgical or medical abortions to terminate the pregnancy in order to entirely avoid the risk of having a malformed fetus.
Research suggests that a fetus that has been exposed to Mifepristone alone and is not aborted will continue to develop normally. Exposure of fetuses to Misoprostol can lead to malformations, such as defects in the skull and abnormalities in the limbs (called Mobius Syndrome).However, risk of having a baby with malformations after using Misoprostol is still very small and hardly measurable. 
To compare: the risk of having a child with Down syndrome is 1/1,300 for a 25-year-old woman; at age 35, the risk increases to 1/365. Only pregnant women older than 35 are screened for Down Syndrome indicating that the risk that the fetus has down Syndrome lower than 1 in 365 is considered acceptable. This is a much higher risk than the risk of Mobius Syndrome as a result of the use of Misoprostol (less than 1/1000).
 Kruse, Beth, Suzanne Poppema, Mitchell D. Creinin and Maureen Paul. (2000) Management of side effects and complications in medical abortion. American Journal of Obstetrics and Gynecology 183(2):S65-S75.
 Hamoda, Ashok, Flett, Templeton, A randomized controlled trial of Mifepristone in combination with misoprostol administered sublingually or vaginally for medical abortion up to 13 weeks of gestation. BJOG 2005 Aug; 112(8): 1102-8.
 David S. Newberger, M.D. Down syndrome: Prenatal risk assessment and diagnosis. American Family Physician, Vol. 62/No. 4 (August 15, 2000)