Genetic vaccines encoding pancreatic beta cell antigens can prevent autoimmune (type 1) diabetes when delivered into murine model systems, but there is a need to improve their efficacy. Here, we investigated the effects of intramuscular delivery of DNA coding for the pro-apoptotic protein BAX together with an intracellular or a secreted form of the beta cell antigen glutamic acid decarboxylase (GAD) on diabetes onset and immune responses in non-obese diabetic (NOD) mice. We hypothesized that induction of apoptosis in vaccine-containing cells could lead to GAD tolerance and disease suppression. Remarkably, monitoring of spontaneous diabetes onset indicated that only delivery of DNA coding for secreted GAD and BAX resulted in significant prevention of the disease. Using GFP as a model plasmid-encoded antigen revealed that co-delivery of BAX resulted in the recruitment of GFP-containing dendritic cells (DCs) in the draining lymph nodes and spleen of NOD mice. Furthermore, data indicated that subcellular localization of GAD had an effect on both the number and function of antigen presenting cells (APCs) recruited by BAX as well as on IFN-gamma secretion, and that diabetes suppression was unlikely to be caused by increased T helper 2 (Th2)-like activity. Our results indicate that, under certain conditions, co-delivery of DNA encoding BAX can improve the efficacy of genetic vaccination for prevention of pathogenic autoimmunity via a mechanism likely to involve modulation of antigen presenting cell function. In addition, our data also suggest that properties associated with subcellular localization of an antigen in apoptotic cells can have a significant effect on induced immune responses.