Current evidence suggests a relationship between seasonal influenza viral infection and cardiovascular disease (CVD) complications. Experimentally, animals inoculated with influenza A virus develop thrombotic complications similar to those seen in humans. Conversely, several clinical trials have suggested that influenza vaccination may have a protective effect on CVD. However, the potential mechanisms remain unstudied. In order to study this, we vaccinated six groups of male ApoE−/− mice with 0.36, 1.8, 9 and 45 μg/ml of Vaxigrip (influenza vaccine, Sanofi Aventis), 45 μg/ml of Pneumo23 (Pneumococcus vaccine, Sanofi Aventis) and phosphate-buffered saline (PBS). Animals received one injection and two boosters 3 weeks apart before starting on a high-fat diet for 12 weeks. Plasma was collected pre-immunisation and at termination for profile analysis of antibodies, lipids and cytokines. Analysis of atherosclerosis development was carried out using paraffin sections of the brachiocephalic artery. We observed an increase in anti-influenza IgG1 but not in IgG2a, IgG2b, IgA or IgM in any of the groups. Animals that received Pneumo23 vaccine only showed increased levels of vaccine-specific IgM. No significant changes in plasma levels of lipids were noted. Animals vaccinated with 45 μg/ml Vaxigrip developed smaller atherosclerotic lesions with lower lipid content but were richer in inflammatory cells and collagen than control animals. Other groups showed no significant differences in plaque area, lumen and tunica media area. Animals vaccinated with 45 μg/ml Vaxigrip showed lower levels of interleukin (IL) 2, interferon γ and IL-17 and higher levels of IL-4. Our results suggest that vaccination against influenza may protect against CVD by inducing stable and smaller atherosclerotic plaques.