Progress of research on stem cells including their genetic modifications allowed to obtain very promising results. However, one of the main barriers that (ex vivo) therapy has been encountered was delivery of genetic construct to the target cell. As well plasmids (delivered with using physico-chemical methods) as viral vectors have its prominent place at preparations aimed to implant genetically modified stem cells (auto- or allogenic origin) to recipient organ. Genetic modifications involve therapeutic, reporter or regulatory genes which may help to implantation of stem cells itself, to limit inflammatory process or apoptosis, to enhance physiological function of damaged organs/tissues. This review presents a progress in invention of novel genetic constructs and indicates main trends for application of genetically modified stem cells as therapeutic agents for either congenital or acquired pathologies.