Transgenic animals are new and important models for the study of candidate genes in hypertension research as well as in other fields of medicine. For detailed genetic characterization of the transgenic animals, and to account for the symptoms arising from the insertion of transgenes in the genome, it is essential to identify these insertion sites. In this study, the insertion sites of the transgenes of candidate genes for hypertension were identified by fluorescence in situ hybridization (FISH) after G-banding of the chromosomes in transgenic rats and mice. This technique combines high resolution G-banding and fluorescence in situ hybridization for the mapping of four different candidate genes in six different transgenic rats as well as three different mouse transgenic lines. The presented results will help to draw conclusions about the influence of the respective integration site on transgene expression.