One of the major worries in society concerning designer babies is that it could turn into eugenics.  Where we would select out for only the prettiest, most intelligent, disease free individuals.  Most geneticists don't think that society would ever go that far but they can not speak for the entire human race because at one point some person, some where with the right capabilities would start the process.  People fear that another Hitler could emerge, but be much more powerful.

A second ethical issue involved in this debate is abortion.  If you found that your child was found to have a disease that doesn't have a cure and could lead to a poor quality of life through prenatal screening, would you have an abortion.  This is a very important issue for physicians who worry that their prenatal diagnosis may lead to abortion of the fetus.  Many Jewish geneticists believe that prenatal diagnosis should not be done if the diagnosis may lead to abortion.  They believe instead of pre-marital counseling.  Where a man and a woman should be genetically tested before marriage and if found that they are both carriers of a genetic disorder that they should not be married.  Another practice that the Jewish community endorses is pre-implantation screening.  This entails practices similar to IF but before the embryos are implanted they are screened for genetic disorders.  Only healthy embryos are implanted.  In the Jewish tradition only an embryo implanted in a uterus is considered living so discarding of the inflicted embryos is not considered abortion. 

Many people's views are mixed.  They believe that screening for diseases is okay but not for determining sex of the baby.  Or sex selection is okay if there is a genetic disorder that inflicts only males such as hemophilia.
The ethical debate is only going to get more intense as more and more information and technology becomes available.

An important in the ethical discussion is that women have rights to make their own decisions.  If a woman wishes to maintain a pregnancy that is doomed, she has the right to do so even if genetic testing told her that the child's quality of life could be very low.  In these instances, genetic counseling is that much more important.  Since so many of these procedures are new what then is the implication of experimenting with the genes trying to save a life that ends up shortening the child's life or reducing their quality of life..  This idea raises many questions for the parents regarding the safety of their child when performing gene therapy.