Vaxfectin, a cationic lipid-based adjuvant, when combined with a seasonal influenza protein vaccine has been reported to enhance predominantly either antibody or cellular responses depending upon the ratio of adjuvant to antigen. Preliminary physical characterization showed that particle size was dependent on the antigen to Vaxfectin ratio. In an effort to identify potential predictive markers helpful in formulation development, a panel of biomarkers was assayed both at the site of administration and in the serum. Local upregulation of IFN-gamma, IL-6, Cxcl9, CCL2, TNF-alpha, CD274 as well as Toll-like receptor pathway transcripts MyD88, TLR2, TLR3 and TLR9 was observed. Also, systemic levels of IL-6, TNF-alpha and CCL2 were elevated in response to Vaxfectin formulation in a ratio-dependent manner. These results have identified biomarkers that may be useful in testing Vaxfectin-protein formulations to produce balanced humoral and cell-mediated immune responses.