The aim of this study was to investigate the mechanisms exerted by complexed linear DNA vectors encoding Interleukin (IL-) 12 and IL-18 applied in vivo in horses. To enable this first suitable biomarkers for the acute immune response of horses were evaluated. Within these, 15 monoclonal antibodies for cytokines of different species were evaluated for reactivity with equine cytokines. To accurately employ the cytokines and further selected parameters as biomarkers for treatment effects, internal controls were included and evaluated for influencing physiological factors. The age, sex and type of the horses influenced leukocyte composition, cell morphology and cytokine release by peripheral blood mononuclear cells (PBMC) ex vivo. Linear DNA vectors encoding equine IL-12/-18 complexed with transfection reagent (SAINT-18) or comparative substances (SAINT-18 only, complexed nonsense DNA, complexed nonsense DNA without CpG) were applied to 24 healthy horses. All groups receiving complexed linear DNA vectors showed a systemic and local inflammatory response. This appeared basically independent of expression and CpG content of the DNA applied. Moreover, expressions of IL-12 and IL-18 enhanced immunostimulation and induced Th1 downstream mediators. Grey horses showed significantly fewer effects of DNA-treatments and were classified non-responders to immunostimulatory effects of linear DNA complexed with SAINT-18.