Adeno-associated virus (AAV) derived vectors are considered highly eligible vehicles for human gene therapy. Not only do they possess many great potential for clinical applications due to their wide range of tissue targets but also their excellent preclinical safety profile makes them particularly suitable candidates for treating serious diseases. Initial clinical trials have yielded encouraging results and prompted further improvements in their design and methods of production. Many studies have been performed to modify the tropism of recombinant (r)AAV by capsid modification. However, the precise control of spatial and temporal gene expression, which may be important in determining the safety and efficacy of gene transfer, lies in a rational choice and a subtle combination of various regulatory genetic elements to be inserted into the expression cassette. Moreover, new strategies based on such genetic sequences open new perspectives for enhancing vector genome persistence, disrupting or reducing pathogenic gene expression and even targeting genes.