The positive benefits are pretty obvious, so here is info on the negative effects…

If gene therapy was done to a certain extent could it alter the human gene pool for good? And also would this form of treatment be a luxury only for the rich which could very well make the rich, richer and make the poor, poorer. http://www.ndsu.nodak.edu/instruct/mcclean/plsc431/students/eric.htm

Some people are concerned that gene therapy will be used to create a superior race….Some groups claim that regulations will be hard to control, even with laws there is the possibility gene therapy could become available on the black market. It could be used for any genetically linked trait such as eternal appearance, personality, or physical enhancement. These concerns will have to be dealt with in time.
The cost of gene therapy is high at this time and could be a concern for families with that need lifelong treatment and do not have health care. Invasion of privacy is also a concern for many. Insurance companies could make it mandatory to have genetic screening before a policy before they issue a policy. This could cause discrimination to families with genetic diseases. Or potential employers could question a person’s genetic background and pass them up for a promotion or job. These are all good reasons to use gene therapy and eliminate the controversy before it starts.
The last and most important concern is the risk of the procedure. It is still in the developmental stage. Finding the precise location of the defected gene is still under research. Any miscalculation could cause a risk of a new disease such as cancer to form.
http://www.ndsu.nodak.edu/instruct/mcclean/plsc431/students98/fleck.htm

Gene therapy sounds like a dream come true for those with muscular dystrophy or other diseases. But gene therapy could also turn into gene doping for athletes desiring that extra boost of energy or speed to win. If gene therapy is poised to become a practical medical treatment, gene doping for personal wants is not far behind. In truth, the start of research toward genetically enhancing muscle size and strength was not focused on serving elite athletes.
http://www.helium.com/items/1052518-weighing-the-pros-and-cons-of-gene-therapy

Gene Therapy is not without its downfalls. There are media reports of gene therapy going terribly wrong. On September 17th, 1999, an 18 year old boy by the name of Jesse Gelsinger died as a direct result of his voluntary participation in a trial of gene therapy. Jesse had a rare genetic disorder called Ornithine Transcarbamylase Deficiency (OTC), which prevented his body from ridding itself of Ammonia. Jesse received a high dose of Adenovirus’. Scientists thought the worst symptom Jesse would experience was an inflammation of the Liver. The Adenovirus was injected into his bloodstream, resulting in multiple organ failure, and led to his death four days later. (www.newsweekly.com.au/article s/2000aug12_bio.html)

Gene Therapy is a largely untested science. It raises ethical, medical and religious issues. It has been reported that some forms of gene therapy have actually caused Cancer in some patients. Recently, almost thirty gene therapy trials in the USA were forced to a halt. The trials reportedly caused Leukaemia in two young boys. Before this was discovered, the actual test was hailed as one of the first remarkable successes in the field of gene therapy. The trials aimed to find a cure for X-chromosome-linked Severe Combined Immunodeficiency, or X-SCID.
(http://www.newscientist.com/a rticle.ns?id=dn3271)

Additional downfalls of gene therapy include the fact that it is simply unnatural. Biotechnologists are playing with nature. Countless animals are mutilated and/or killed for experiments, where they experience great pain and suffering. Finally, animals are simply a poor model of human genetic diseases.
(www.ifgene.org/proscons.htm)
http://www.helium.com/items/166289-weighing-the-pros-and-cons-of-gene-therapy?page=3