Just your genes...?
Gene therapy is only used on non-reproductive (somatic) cells - that is, any cells other than sperm or egg cells.
The genetic change introduced by the therapy is not passed on to the patient's children. For the ‘new’ gene to be passed on to the patient's offspring, germline gene therapy has to occur - that is, a permanent transfer of the gene into the patient’s egg or sperm cells. This is illegal in Australia.
Currently, there is insufficient knowledge about the possible consequences for future generations of the use of these therapeutic techniques. There are a number of ethical considerations that would need to be taken into account before the therapy can be used widely.
These include weighing up the potential benefits for the patient with the harm that might be done to them or their children, and considering under what conditions it would be justifiable to make changes so that they do not occur in future generations.
The genetics underlying most conditions is quite complex and completely eradicating a particular form of a gene we believe to cause disease may have far-reaching consequences for future generations. That particular gene change may actually be advantageous in some circumstances.
For example, people who carry a copy of the allele that causes sickle cell anaemia have an increased resistance to the deadly infectious disease, malaria. If the sickle cell allele is removed from the population, many more might die in areas affected by malaria.
Watch an animation from the Walter and Eliza Hall Institute of Medical Research that depicts aspects of the haemoglobin molecules and the mutant form that causes the disease sickle cell anaemia: http://www.wehi.edu.au/education/wehi-tv/dna/haemoglobin.html
Gene therapies on humans are allowed under Australian legislation, but the National Health and Medical Research Council (NHMRC) sets strict guidelines for conducting trials and gene therapies on humans. These can be downloaded here:
Guidelines for Ethical Review of Research Proposals for Human Somatic Cell Gene Therapy and Related Therapies (1999) http://www.nhmrc.gov.au/publications/synopses/e38syn.htm