In the debate regarding the different possibilities for gene therapy, it is presupposed that the manipulations are limited to the nuclear genome (nDNA). Given recent advances in genetics, mitochondrial genome (mtDNA) and diseases must be considered as well. In this paper, we propose a three dimensional framework for the ethical debate of gene therapy where we add the genomic type (nDNA vs. mtDNA) as a third dimension to be considered beside the paradigmatic dimensions of target cell (somatic vs. germ-line) and purpose (therapeutic vs. enhancement). Somatic gene therapy can be viewed today as generally accepted, and we review the contemporary arguments surrounding it on the basis of bioethical-pragmatic, socio-political and deontological classifications. Many of the supposed ethical questions of somatic gene therapy today are not new; they are well-known issues of research ethics. We also critically summarize the different international perspectives and the German ethical discussion regarding manipulations of germ-line cells.