Methods for preventing, delaying the onset of, or treating rejection of an allograft using a DNA vaccine, where the vaccine can comprise a polynucleotide encoding a pro-apoptotic protein, like BAX and/or a polynucleotide encoding an autoantigen or donor antigen, like secreted glutamic acid decarboxylase 55. Administering one of the DNA vaccines to a transplant recipient, as described herein, can induce a donor specific tolerogenic response.