Dr. Muzammil Siddiqi, former president of the Islamic Society of North America, states the following: “According to all jurists the abortion is allowed in the situation when mother’s life is at an actual risk.
In the case of multiple embryos, it is not permissible to kill some and save some. However, if there are some unhealthy embryos that might cause death to others, then some competent doctors should decide to remove the dangerous embryo. But this must be done with great care and only in the case of actual, not perceived, danger.
It is the basic principle of the Shari`ah that when there are two harms, then one should choose the lesser harm or Akhaff Ad-Dararayn.
In this situation, there are two harms present: either to lose all the embryos or lose some. If this is the only choice, then the dangerous and unhealthy embryos can be aborted.
If the case is of actual risk to the life of the mother, there is no time limit. Before the birth any time, abortion can be done as long as the risk is actual, not just imagined or perceived.”