Genetic immunisation is emerging as a safe and specific means of eliciting prophylactic and therapeutic immune responses. Just as the immune response to various infectious agents will differ based on the aetiology of the infection and nature of antigenic determinants, so does the immune response following genetic immunisation. This review will discuss the impact of vector selection and antigen structure on genetic immunisation. Comparative analyses of plasmid DNA (pDNA), adenovirus (Ad) and vaccinia virus vaccines have demonstrated that each vector system is associated with a unique outcome following immunisation. Similarly, re-targeting cytosolic protein to different cellular compartments can dramatically affect the subsequent immune response. Thus, to design an effective genetic vaccine, one must consider both the biology of the vaccine vector/antigen combination and the biology of the pathogen.