Stem cell and gene therapy approaches have held out much hope for the development of new tools to treat disease. Therapeutic approaches based on these methods have only rarely found their way into the clinic. The linking of stem cell therapy with selective gene therapy enhances therapeutic options for the regeneration or replacement of diseased or missing cells. This review focuses on the rationale and preliminary results of combining stem cell and gene therapy. Special emphasis is placed on various molecular techniques currently used to genetically engineer stem cells. Viral and nonviral genes delivering technologies are detailed as are techniques for the modulation of gene expression in the context of stem cell recruitment and differentiation. Finally potential clinical applications for this new therapeutic strategy are discussed.